DNA project sources and coverage¶
This dated survey separates original methods, upstream software, skills, MCP services and DNAKit adapters. Listing a project does not mean its software is installed or its results are validated.
Snapshot: 2026-09-20. Projects/sources: 419. Logged searches: 88.
The search extends beyond the initial 11 areas. It remains a versioned survey, not a claim to have enumerated every DNA paper or project.
1) BOLE¶
Wang Zishuai, Liang Chongxiao, Zhang Yanlin, Zhou Rong, Zhang Xiaoai, Wei Wenkang and Li Kui describe a breeding agent framework. A public benchmark/evidence repository was found; a complete runnable framework or documented callable API was not verified. DNAKit records these sources without claiming a BOLE reimplementation. The local relationship and ridge-prediction functions independently implement the cited mathematical methods.
BOLE (2026) · VanRaden (2008) · Endelman (2011)
BOLE benchmark evidence · 335-project review / 补充清单审核
2) Coverage¶
| Domain / 方向 | Project records / 项目记录数 |
|---|---|
序列处理与格式 (sequence) |
57 |
测序、质控与覆盖度 (sequencing) |
21 |
比对与参考序列 (alignment) |
10 |
基因组组装 (assembly) |
15 |
泛基因组与图基因组 (pangenome) |
10 |
基因识别与功能注释 (annotation) |
36 |
启动子、增强子与调控 (regulation) |
26 |
小变异与结构变异 (variants) |
41 |
疾病、肿瘤与药物基因组 (clinical) |
42 |
育种、性状与种质资源 (breeding) |
21 |
关联分析、遗传力与因果遗传 (gwas) |
19 |
群体遗传与祖源 (population) |
39 |
比较基因组与系统发育 (comparative) |
32 |
遗传与进化模拟 (simulation) |
4 |
多倍体与单倍型 (polyploid) |
9 |
法医、亲缘与 DNA 鉴定 (forensics) |
13 |
物种、食品与环境溯源 (traceability) |
8 |
古 DNA 与损伤 (ancient-dna) |
6 |
环境 DNA 与保护遗传 (edna) |
6 |
微生物、宏基因组与耐药 (metagenomics) |
42 |
甲基化与表观遗传 (epigenomics) |
39 |
染色质空间结构与接触图 (3d-genomics) |
7 |
单细胞 DNA 与多组学 (single-cell-dna) |
6 |
空间基因组 (spatial-genomics) |
1 |
基因编辑与脱靶 (crispr) |
27 |
合成生物学与序列优化 (synthetic) |
18 |
复制、损伤修复与端粒 (replication-repair) |
5 |
功能筛选与变异效应实验 (functional-assays) |
18 |
重复与移动遗传元件 (repeats) |
11 |
病毒与噬菌体基因组 (viral-genomics) |
4 |
线粒体与叶绿体基因组 (organellar) |
2 |
DNA 纳米结构与分子力学 (nanotechnology) |
4 |
DNA 数据存储与编码 (dna-storage) |
8 |
DNA 链置换与分子计算 (strand-displacement) |
5 |
DNA 基础模型与表示 (models) |
21 |
数据库与知识检索 (databases) |
15 |
智能体、Skills、MCP 与复现 (workflows) |
48 |
3) Who is credited by each integration?¶
Authors below are project/paper credits, not DNAKit authorship claims. Repository ownership is shown when individual authors were not verified. Original workflow citations remain in each skill's UPSTREAM.json and SKILL.md.
| Project / 项目 | Authors and sources / 作者与来源 | DNAKit integration / 本地接口或状态 |
|---|---|---|
| ABC enhancer-gene model | https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction authors and contributors; individual paper authors are not inferred | Related local workflows: causal-genomics-effector-gene-prioritization |
| ABRicate | https://github.com/tseemann/abricate authors and contributors; individual paper authors are not inferred | abricate-screen |
| ADMIXTOOLS 2 | uqrmaie1 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: population-genetics-population-structure |
| ADMIXTURE | ADMIXTURE authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Aldy | https://github.com/0xTCG/aldy authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| AlphaGenome API | https://github.com/google-deepmind/alphagenome authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| AlphaGenome Research | https://github.com/google-deepmind/alphagenome_research authors and contributors; individual paper authors are not inferred supplied source 1 | dnakit.predictions.api.predict_properties |
| AlphaMate | AlphaGenes 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: ecological-genomics-conservation-genetics |
| AlphaSimR | R. Chris Gaynor, Gregor Gorjanc, John M. Hickey paper 1 supplied source 1 | Related local workflows: plant-genomics |
| AMRFinderPlus | ncbi项目作者与贡献者；terms of the United States Copyright Act. It was written as part of；thus cannot be copyrighted. This software/database is freely available paper 1 paper 2 | amrfinder-nucleotide; Related local workflows: metagenomics-amr-detection |
| ANGSD | https://github.com/ANGSD/angsd authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| AnnotSV | https://github.com/lgmgeo/AnnotSV authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Anthropic Life Sciences | https://github.com/anthropics/life-sciences authors and contributors; individual paper authors are not inferred | MCP: pubmed-anthropic; MCP: opentargets-platform; MCP: 10x-genomics; 3 bundled Skills |
| arcasHLA | https://github.com/RabadanLab/arcasHLA authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ArchR | https://github.com/GreenleafLab/ArchR authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ARIBA | https://github.com/sanger-pathogens/ariba authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ASCAT | https://github.com/VanLoo-lab/ascat authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ASTRAL | https://github.com/smirarab/ASTRAL authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| AUGUSTUS | https://github.com/Gaius-Augustus/Augustus authors and contributors; individual paper authors are not inferred supplied source 1 | augustus-genes |
| AutoBA | https://github.com/Panomica/AutoBA authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| AutoPVS1 | https://github.com/JiguangPeng/autopvs1 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| AWS Kiro Life Sciences | https://github.com/aws-samples/sample-kiro-power-life-sciences authors and contributors; individual paper authors are not inferred | MCP: kiro-genomics; MCP: kiro-model-organisms; MCP: kiro-epigenomics; MCP: kiro-agriculture; MCP: kiro-ecology; MCP: kiro-clinical; MCP: kiro-pipelines; 1 bundled Skills |
| Azimuth | https://github.com/MicrosoftResearch/Azimuth authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BAGEL2 | https://github.com/hart-lab/bagel authors and contributors; individual paper authors are not inferred | Related local workflows: crispr-screens-bagel-essentiality, crispr-screens-screen-qc |
| Bakta | https://github.com/oschwengers/bakta authors and contributors; individual paper authors are not inferred paper 1 | bakta-annotation |
| Barrnap | tseemann/barrnap authors and contributors | barrnap-rrna |
| Basenji | https://github.com/calico/basenji authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BCFtools | https://github.com/samtools/bcftools authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.ngs.call_variants |
| BE-Hive bystander model | https://github.com/maxwshen/be_predict_bystander authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BEDTools | https://github.com/arq5x/bedtools2 authors and contributors; individual paper authors are not inferred | Related local workflows: cite-encode |
| BGLR | Paulino Pérez, Gustavo de los Campos paper 1 paper 2 | Related local workflows: plant-genomics |
| BioCoder | https://github.com/gersteinlab/BioCoder authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| BioContextAI Knowledgebase MCP | https://github.com/biocontext-ai/knowledgebase-mcp authors and contributors; individual paper authors are not inferred | MCP: biocontext-kb |
| BioContextAI Registry | https://github.com/biocontext-ai/registry authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| bioframe | https://github.com/open2c/bioframe authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BioinfoMCP | florensiawidjaja/BioinfoMCP authors and contributors paper 1 | Reference only; not integrated |
| Bioinformatics MCP | raonyguimaraes/bioinformatics-mcp authors and contributors | Reference only; not integrated |
| BioMCP | genomoncology项目作者与贡献者；Copyright (c) 2025 Ian Maurer；The above copyright notice and this permission notice shall be included in all | MCP: biomcp; 1 bundled Skills; Related local workflows: clinical-databases-clinvar-lookup, variant-interpretation |
| BioMCP TypeScript | yeyuan98项目作者与贡献者；"Licensor" shall mean the copyright owner or entity authorized by；the copyright owner that is granting the License. paper 1 | Related local workflows: clinical-databases-clinvar-lookup |
| Biopython | https://github.com/biopython/biopython authors and contributors; individual paper authors are not inferred supplied source 1 | dnakit.bioinformatics.reads.read_fastx; dnakit.bioinformatics.alignment.read_alignment; dnakit.bioinformatics.motifs.build_motif |
| bioSkills | GPTomics项目作者与贡献者；Copyright (c) 2026 GPTomics；The above copyright notice and this permission notice shall be included in all | 331 bundled Skills; Related local workflows: metagenomics-kraken, methylation-calling, variant-calling-deepvariant |
| Biostrings | Biostrings authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BioThings MCP | https://github.com/longevity-genie/biothings-mcp authors and contributors; individual paper authors are not inferred | MCP: biothings |
| BioTools MCP | neuralx-dev 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: blast-searches, phylo-tree-io |
| bioutils | https://github.com/biocommons/bioutils authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Bismark | FelixKrueger项目作者与贡献者 | Related local workflows: methylation-bismark-alignment, methylation-calling |
| BOLD Data Portal API | BOLD Data Portal API authors and contributors paper 1 | Related local workflows: ecological-genomics-edna-metabarcoding |
| BOLE | Zishuai Wang, Chongxiao Liang, Yanlin Zhang, Rong Zhou, Xiaoai Zhang, Wenkang Wei, Kui Li paper 1 paper 2 paper 3 supplied source 1 | Related local workflows: causal-genomics-heritability-partitioning, plant-genomics, workflows-gwas-pipeline |
| Borzoi | https://github.com/calico/borzoi authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| Bowtie2 | https://github.com/BenLangmead/bowtie2 authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.ngs.map_reads |
| BPNet | https://github.com/kundajelab/bpnet authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Bracken | jenniferlu717项目作者与贡献者；Copyright (C) 2008 Free Software Foundation, Inc. http://fsf.org/；(1) assert copyright on the software, and (2) offer you this License paper 1 supplied source 1 | Related local workflows: metagenomics-abundance |
| BRAKER | https://github.com/Gaius-Augustus/BRAKER authors and contributors paper 1 paper 2 paper 3 paper 4 | Related local workflows: genome-annotation-eukaryotic-gene-prediction |
| BRAKER4 | https://github.com/Gaius-Augustus/BRAKER4 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BrAPI MCP | https://github.com/cyanheads/brapi-mcp-server authors and contributors; individual paper authors are not inferred | MCP: brapi |
| BSgenome | BSgenome authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| bsseq | https://github.com/hansenlab/bsseq authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| BUSCO | BUSCO authors and contributors; individual paper authors are not inferred paper 1 | busco-proteins; busco-genome |
| BV-BRC MCP | BV-BRC项目作者与贡献者 | Related local workflows: microbial-genome-characterization |
| BWA-MEM2 | https://github.com/bwa-mem2/bwa-mem2 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| bwa-meth | https://github.com/brentp/bwa-meth authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| CADD | https://github.com/kircherlab/CADD-scripts authors and contributors; individual paper authors are not inferred supplied source 1 supplied source 2 supplied source 3 | Reference only; not integrated |
| Caduceus | https://github.com/kuleshov-group/caduceus authors and contributors; individual paper authors are not inferred | Related local workflows: caduceus |
| CalicoST | raphael-group项目作者与贡献者；Copyright (c) 2023, Princeton University；1. Redistributions of source code must retain the above copyright notice, this | Related local workflows: copy-number-allele-specific-copy-number |
| Canu | https://github.com/marbl/canu authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Cas-OFFinder | https://github.com/snugel/cas-offinder authors and contributors paper 1 | cas-offinder; Related local workflows: crispr-screens-library-design |
| Cas-OFFinder bulge branch | https://github.com/pnucolab/cas-offinder-2 authors and contributors paper 1 | Related local workflows: crispr-screens-library-design |
| hubayirp/agentic-science | hubayirp/agentic-science contributors | 3 bundled Skills |
| NVIDIA-BioNeMo/bionemo-agent-toolkit | NVIDIA Corporation and contributors | 3 bundled Skills |
| ClawBio/ClawBio | ClawBio contributors | 23 bundled Skills; Related local workflows: amplicon-qc, analyze-fasta, ancestry-risk-profiler, article-data-fetcher, bioconductor-bridge, crispr-screen-triage, eqtl-catalogue-region-fetch, equity-scorer, galaxy-bridge, gwas-catalog-region-fetch, illumina-bridge, ld-1000g-region-compute, locuscompare-region-render, multiqc-reporter, nfcore-sarek-wrapper, rare-high-impact-variants, recombinator, sample-qc-triage, seq-wrangler, ukb-ppp-region-fetch, wgs-prs |
| DamLabResources/damlab-skills | DamLabResources/damlab-skills contributors | 2 bundled Skills |
| google-deepmind/science-skills | Copyright 2026 Google LLC | 9 bundled Skills |
| companion-inc/feynman | companion-inc/feynman contributors | 1 bundled Skills |
| muwenbo/genetic-counseling-skills | muwenbo/genetic-counseling-skills contributors | 6 bundled Skills |
| juanesarango/isabl-mcp | juanesarango/isabl-mcp contributors | 8 bundled Skills |
| tanaylab/misha | tanaylab/misha contributors | 1 bundled Skills |
| KalarisLabs/Myriad | MYRIAD by Srihari Muralikrishnan and Kalaris Labs. https://github.com/KalarisLabs/myriad | 1 bundled Skills |
| htlin222/ngs-tertiary-analysis-skills | htlin222/ngs-tertiary-analysis-skills contributors | 1 bundled Skills |
| Li-Chia-ching/Plant-qPCR-Agent-Skill | Li-Chia-ching/Plant-qPCR-Agent-Skill contributors | 1 bundled Skills |
| Xuzhen-Li/bioinfo-agent-skills | Xuzhen-Li/bioinfo-agent-skills contributors | 6 bundled Skills |
| Li-Chia-ching/Polyploid-GeneFamily-AI-Pipeline | Li-Chia-ching/Polyploid-GeneFamily-AI-Pipeline contributors | 1 bundled Skills |
| Ynzuses/research-skills-suite | Ynzuses/research-skills-suite contributors | 2 bundled Skills |
| jaechang-hits/SciAgent-Skills | jaechang-hits; credited K-Dense-AI and Biomni contributors | 21 bundled Skills |
| mims-harvard/ToolUniverse | ToolUniverse contributors, mims-harvard | MCP: tooluniverse; 35 bundled Skills |
| ccsmeth | https://github.com/PengNi/ccsmeth authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Cello | https://github.com/CIDARLAB/cello authors and contributors | Reference only; not integrated |
| Cello v2 | https://github.com/CIDARLAB/Cello-v2 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Centrifuge | https://github.com/DaehwanKimLab/centrifuge authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Chamaeleo | ntpz870817/Chamaeleo authors and contributors paper 1 | dnakit.genomics.encode_dna_storage; dnakit.genomics.decode_dna_storage; Related local workflows: dnakit-dna-storage |
| ChAMP | ChAMP authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| CheckM2 | https://github.com/chklovski/CheckM2 authors and contributors; individual paper authors are not inferred paper 1 | checkm2-predict; Related local workflows: checkm2 |
| chewBBACA | https://github.com/B-UMMI/chewBBACA authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| CHISEL | raphael-group项目作者与贡献者；Copyright (c) 2019, Princeton University；1. Redistributions of source code must retain the above copyright notice, this paper 1 | Related local workflows: copy-number-allele-specific-copy-number |
| Chorus | https://github.com/pinellolab/chorus authors and contributors | MCP: chorus |
| ChromBPNet | https://github.com/kundajelab/chrombpnet authors and contributors paper 1 paper 2 paper 3 supplied source 1 | Related local workflows: atac-seq-footprinting |
| chromVAR | chromVAR authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Clair Skills | HKU-BAL项目作者与贡献者 | Related local workflows: long-read-sequencing-clair3-variants |
| Clair3 | HKU-BAL项目作者与贡献者；Copyright 2021 The University of Hong Kong, Department of Computer Science；1. Redistributions of source code must retain the above copyright notice, this paper 1 paper 2 paper 3 paper 4 | Related local workflows: long-read-sequencing-clair3-variants |
| ClassifyCNV | https://github.com/Genotek/ClassifyCNV authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| CNVkit | etal项目作者与贡献者；Copyright (c) 2013-2018 Eric Talevich；Copyright (c) 2013-2018 University of California | Related local workflows: copy-number-cnvkit-analysis |
| coloc | https://github.com/chr1swallace/coloc authors and contributors; individual paper authors are not inferred supplied source 1 supplied source 2 | Reference only; not integrated |
| Control-FREEC | https://github.com/BoevaLab/FREEC authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Cooler | open2c项目作者与贡献者；Copyright (c) 2015-2023, Cooler developers；1. Redistributions of source code must retain the above copyright notice, this paper 1 paper 2 | Related local workflows: hi-c-analysis-hic-data-io, hi-c-analysis-matrix-operations |
| Cooltools | open2c项目作者与贡献者；Copyright (c) 2017 Cooltools developers；The above copyright notice and this permission notice shall be included in all paper 1 | Related local workflows: hi-c-analysis-compartment-analysis, hi-c-analysis-tad-detection |
| CRABS | G.-J. Jeunen, E. Dowle, J. Edgecombe, U. von Ammon, N. J. Gemmell, H. Cross paper 1 | Related local workflows: ecological-genomics-edna-metabarcoding |
| CREsted | https://github.com/aertslab/CREsted authors and contributors paper 1 paper 2 | Reference only; not integrated |
| CRISPOR | https://github.com/maximilianh/crisporWebsite authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| CRISPR-GPT public light | https://github.com/cong-lab/crispr-gpt-pub authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| crisprDesign | https://github.com/crisprVerse/crisprDesign authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| CRISPResso2 | https://github.com/pinellolab/CRISPResso2 authors and contributors paper 1 | crispresso2-amplicon; Related local workflows: crispr-screens-crispresso-editing |
| CRISPRitz | https://github.com/pinellolab/CRISPRitz authors and contributors | Related local workflows: crispr-screens-library-design |
| CRISPRme | https://github.com/pinellolab/CRISPRme authors and contributors paper 1 | Reference only; not integrated |
| crisprScore | https://github.com/crisprVerse/crisprScore authors and contributors paper 1 paper 2 | Related local workflows: crispr-screens-library-design |
| Cutadapt | https://github.com/marcelm/cutadapt authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| cuteSV | https://github.com/tjiangHIT/cuteSV authors and contributors; individual paper authors are not inferred supplied source 1 supplied source 2 | Reference only; not integrated |
| cyvcf2 | https://github.com/brentp/cyvcf2 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DADA2 | https://github.com/benjjneb/dada2 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DAS Tool | https://github.com/cmks/DAS_Tool authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| deepDNAshape | JinsenLi/deepDNAshape authors and contributors | Reference only; not integrated |
| DeepSignal | https://github.com/bioinfomaticsCSU/deepsignal authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DeepSTARR | https://github.com/bernardo-de-almeida/DeepSTARR authors and contributors paper 1 paper 2 paper 3 paper 4 paper 5 | Reference only; not integrated |
| deepTools | https://github.com/deeptools/deepTools authors and contributors; individual paper authors are not inferred | Related local workflows: cite-encode |
| DeepVariant | google项目作者与贡献者；Copyright 2020 Google LLC.；1. Redistributions of source code must retain the above copyright notice, this paper 1 paper 2 | Related local workflows: variant-calling-deepvariant |
| DELLY | https://github.com/dellytools/delly authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| DIAMOND | https://github.com/bbuchfink/diamond authors and contributors; individual paper authors are not inferred paper 1 | diamond-blastp; diamond-blastx |
| DMRcate | DMRcate authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| dmrseq | dmrseq authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DNA-Aeon | MW55/DNA-Aeon authors and contributors paper 1 | Reference only; not integrated |
| DNA Cauldron | https://github.com/Edinburgh-Genome-Foundry/DnaCauldron authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DNA Features Viewer | https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DNA Fountain | https://github.com/TeamErlich/dna-fountain authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DNABERT2 | https://github.com/MAGICS-LAB/DNABERT_2 authors and contributors; individual paper authors are not inferred | Related local workflows: dnabert2 |
| DNA Chisel | https://github.com/Edinburgh-Genome-Foundry/DnaChisel authors and contributors supplied source 1 | Related local workflows: codon-usage |
| DNAplotlib | https://github.com/VoigtLab/dnaplotlib authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DNAscent | https://github.com/MBoemo/DNAscent authors and contributors paper 1 paper 2 paper 3 paper 4 | Reference only; not integrated |
| DNAshapeR | TsuPeiChiu/DNAshapeR authors and contributors | Reference only; not integrated |
| DNASpiderWeb | HaolingZHANG/DNASpiderWeb authors and contributors | Reference only; not integrated |
| dnastore | ihh/dnastore authors and contributors paper 1 | Reference only; not integrated |
| DNA Weaver | https://github.com/Edinburgh-Genome-Foundry/DnaWeaver authors and contributors | Reference only; not integrated |
| Dorado | https://github.com/nanoporetech/dorado authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| DR4DNA | umr-ds/DR4DNA authors and contributors | Reference only; not integrated |
| DrugZ | https://github.com/hart-lab/drugz authors and contributors; individual paper authors are not inferred | drugz-unpaired; Related local workflows: crispr-screens-drugz-chemogenomic |
| DSS | DSS authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| EBI Tools MCP (QuentinCody) | https://github.com/QuentinCody/ebi-tools-mcp-server authors and contributors; individual paper authors are not inferred | MCP: ebi-tools |
| EDTA | https://github.com/oushujun/EDTA authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| eggNOG-mapper | https://github.com/eggnogdb/eggnog-mapper authors and contributors; individual paper authors are not inferred paper 1 paper 2 | eggnog-proteins |
| EIGENSOFT | https://github.com/DReichLab/EIG authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ENCODE Toolkit | ammawla项目作者与贡献者；Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/；with two steps: (1) assert copyright on the software, and (2) offer paper 1 paper 2 | MCP: encode-toolkit; 16 bundled Skills; Related local workflows: accessibility-aggregation, hic-aggregation, methylation-aggregation |
| Enformer | https://github.com/google-deepmind/deepmind-research/tree/master/enformer authors and contributors; individual paper authors are not inferred | dnakit.predictions.api.predict_sequence_properties; dnakit.predictions.api.predict_enformer_benchmark |
| Enrich2 | https://github.com/FowlerLab/Enrich2 authors and contributors paper 1 paper 2 | Reference only; not integrated |
| Ensembl MCP server | https://github.com/cyanheads/ensembl-mcp-server authors and contributors | MCP: ensembl |
| Ensembl VEP | Ensembl项目作者与贡献者；"Licensor" shall mean the copyright owner or entity authorized by；the copyright owner that is granting the License. paper 1 | dnakit.annotation.variants.annotate_variant_vep; dnakit.annotation.variants.annotate_rsid_vep; Related local workflows: variant-annotation |
| EpiDISH | EpiDISH authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| EuroForMix | oyvble 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: variant-calling |
| Evo2 | https://github.com/ArcInstitute/evo2 authors and contributors; individual paper authors are not inferred supplied source 1 | dnakit.predictions.api.predict_properties; Related local workflows: evo2 |
| Exomiser | exomiser项目作者与贡献者 | Related local workflows: clinical-databases-variant-prioritization, rare-disease-diagnosis |
| ExpansionHunter | https://github.com/Illumina/ExpansionHunter authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| f5c | https://github.com/hasindu2008/f5c authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| FACETS | https://github.com/mskcc/facets authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| FastANI | ParBLiSS/FastANI authors and contributors paper 1 | fastani |
| fastp | OpenGene项目作者与贡献者；Copyright (c) 2016 OpenGene - Open Source Genetics Toolbox；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 | Related local workflows: read-qc-fastp-workflow |
| FastQC | FastQC authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.ngs.quality_control |
| fastSTRUCTURE | https://github.com/rajanil/fastStructure authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| FDSTools | Jerrythafast 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: variant-calling |
| FlashFry | https://github.com/mckennalab/FlashFry authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Flye | fenderglass项目作者与贡献者；Copyright (c) 2016, The Regents of the University of California；* Redistributions of source code must retain the above copyright paper 1 paper 2 paper 3 paper 4 | flye-assembly; Related local workflows: genome-assembly-long-read-assembly, genome-assembly-metagenome-assembly |
| FORECasT / SelfTarget | https://github.com/felicityallen/SelfTarget authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| forrel / pedsuite | Magnus Dehli Vigeland / pedsuite contributors; cite Pedigree Analysis in R (2021), ISBN 9780128244302, as requested by pedsuite. | Related local workflows: genomics-study-design |
| FreeBayes | https://github.com/freebayes/freebayes authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Galaxy | https://github.com/galaxyproject/galaxy authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Galaxy Claude Skills (nekrut) | https://github.com/nekrut/galaxy-claude-skills authors and contributors; individual paper authors are not inferred | 1 bundled Skills |
| Galaxy MCP | galaxyproject/galaxy-mcp authors and contributors | Reference only; not integrated |
| GAPIT | Jiabo Wang, Zhiwu Zhang paper 1 supplied source 1 supplied source 2 supplied source 3 supplied source 4 | Related local workflows: workflows-gwas-pipeline |
| GATK | broadinstitute项目作者与贡献者 supplied source 1 | Related local workflows: copy-number-gatk-cnv, gatk-variant-calling |
| GATK-SV | https://github.com/broadinstitute/gatk-sv authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| GCTA | jianyangqt/gcta authors and contributors | gcta-grm; gcta-reml |
| GEMMA | https://github.com/genetics-statistics/GEMMA authors and contributors; individual paper authors are not inferred paper 1 | gemma-lmm |
| GeneChat MCP | natecostello项目作者与贡献者；Copyright (c) 2026 GeneChat Contributors；The above copyright notice and this permission notice shall be included in all | MCP: genechat; Related local workflows: clinical-databases-pharmacogenomics, vcf-basics |
| GeneGPT | https://github.com/ncbi/GeneGPT authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| GenePattern MCP | genepattern/genepattern-mcp authors and contributors | MCP: genepattern |
| geNomad | https://github.com/apcamargo/genomad authors and contributors; individual paper authors are not inferred paper 1 | genomad-mobile-elements; Related local workflows: genomad |
| Genomic Intelligence skill | https://github.com/K-Dense-AI/scientific-agent-skills authors and contributors | 9 bundled Skills; Related local workflows: genomic-intelligence |
| GenomicRanges | GenomicRanges authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| gffutils | https://github.com/daler/gffutils authors and contributors; individual paper authors are not inferred | Related local workflows: genome-intervals-gtf-gff-handling |
| gget | https://github.com/scverse/gget authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| gget MCP | https://github.com/longevity-genie/gget-mcp authors and contributors; individual paper authors are not inferred | MCP: gget |
| Gigwa-MCP | gkanogiannis / Gigwa-MCP contributors; separate attribution to Gigwa and underlying methods. | MCP: gigwa-mcp; 5 bundled Skills; Related local workflows: gigwa-diversity-report, gigwa-explore-instance, gigwa-import-and-qc, gigwa-qc-triage, gigwa-region-scan, plant-genomics, population-genetics-scikit-allel-analysis |
| GrEBI | https://github.com/EBISPOT/GrEBI authors and contributors; individual paper authors are not inferred | MCP: grebi |
| gReLU | https://github.com/Genentech/gReLU authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| GTDB-Tk | Ecogenomics项目作者与贡献者；Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/；(1) assert copyright on the software, and (2) offer you this License paper 1 paper 2 paper 3 paper 4 paper 5 | Related local workflows: gtdb |
| GuideScan CLI | https://github.com/pritykinlab/guidescan-cli authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| GWAS Catalog MCP | gwas-catalog 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: gwas-database |
| GWAS MCP (muslus) | https://github.com/muslus/gwas-mcp authors and contributors; individual paper authors are not inferred | MCP: gwas-mcp |
| GWASpoly | jendelman 项目及贡献者；论文作者见逐项原始引用 paper 1 | Related local workflows: workflows-gwas-pipeline |
| Hail | Hail authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| hap.py | https://github.com/Illumina/hap.py authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| haploqtl | Taylor A. Anderson, Martha A. Sudermann, Darlene M. DeJong, David M. Francis, Christine D. Smart, Martha A. Mutschler paper 1 | 1 bundled Skills; Related local workflows: plant-genomics, population-genetics-population-structure |
| Hartwig HMFtools | https://github.com/hartwigmedical/hmftools authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Helixer | https://github.com/usadellab/Helixer authors and contributors paper 1 paper 2 | Related local workflows: genome-annotation-eukaryotic-gene-prediction |
| hgvs | https://github.com/biocommons/hgvs authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| HiCExplorer | https://github.com/deeptools/HiCExplorer authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| hifiasm | chhylp123项目作者与贡献者；Copyright (c) 2019；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 | hifiasm-assembly; Related local workflows: genome-assembly-hifi-assembly, optimize-hifi-diploid-assembly |
| HipSTR | Thomas Willems (upstream README author); cite Genome-wide profiling of heritable and de novo STR variations, Nature Methods, doi:10.1038/nmeth.4267. paper 1 | Related local workflows: variant-calling |
| HTSlib | https://github.com/samtools/htslib authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| HUMAnN | https://github.com/biobakery/humann authors and contributors; individual paper authors are not inferred | Related local workflows: biobakery-databases |
| HyenaDNA | https://github.com/HazyResearch/hyena-dna authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ichorCNA | https://github.com/broadinstitute/ichorCNA authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| IGV | https://github.com/igvteam/igv authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| inDelphi | https://github.com/maxwshen/inDelphi-model authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| inStrain | https://github.com/MrOlm/inStrain authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| InterProScan | https://github.com/ebi-pf-team/interproscan authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| InterVar | https://github.com/WGLab/InterVar authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| IQ-TREE 2 | https://github.com/iqtree/iqtree2 authors and contributors; individual paper authors are not inferred supplied source 1 supplied source 2 supplied source 3 supplied source 4 | Reference only; not integrated |
| IQ-TREE 3 | iqtree 项目及贡献者；论文作者见逐项原始引用 paper 1 | Related local workflows: phylo-modern-tree-inference |
| JCVI | https://github.com/tanghaibao/jcvi authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Juicebox MCP | aidenlab项目作者与贡献者；Copyright (c) 2016-2019 The Regents of the University of California；The above copyright notice and this permission notice shall be included in all | MCP: juicebox; Related local workflows: hi-c-analysis-hic-visualization |
| Just DNA Agents | https://github.com/dna-seq/just-dna-agents authors and contributors | Reference only; not integrated |
| Kaiju | https://github.com/bioinformatics-centre/kaiju authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| KinDA | DNA-and-Natural-Algorithms-Group/KinDA authors and contributors paper 1 | Reference only; not integrated |
| Kleborate | https://github.com/klebgenomics/Kleborate authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| KMCP | https://github.com/shenwei356/kmcp authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| Kraken2 | DerrickWood项目作者与贡献者；Copyright (c) 2017-2023 Derrick Wood；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 paper 4 supplied source 1 | kraken2-classify; Related local workflows: metagenomics-kraken |
| Liftoff | https://github.com/agshumate/Liftoff authors and contributors paper 1 | liftoff-annotation; Related local workflows: genome-annotation-annotation-transfer |
| Lindel | https://github.com/shendurelab/Lindel authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| LIRICAL | https://github.com/TheJacksonLaboratory/LIRICAL authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Locus | Matthew McNulty (MIT copyright) and Locus contributors; underlying models/data have separate citations. | Related local workflows: ancestry-risk-profiler |
| LUMPY | https://github.com/arq5x/lumpy-sv authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MACS3 | https://github.com/macs3-project/MACS authors and contributors; individual paper authors are not inferred | Related local workflows: cite-encode |
| MAFFT | MAFFT authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.alignment.align_sequences |
| maftools | https://github.com/PoisonAlien/maftools authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MAGeCK | MAGeCK authors and contributors; individual paper authors are not inferred paper 1 | mageck-test; mageck-count |
| Manta | https://github.com/Illumina/manta authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| mapDamage | ginolhac 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: grapevine-adna |
| MAPpoly | mmollina 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: polyploid-gene-family-cloning |
| MaveDB API | https://github.com/VariantEffect/mavedb-api authors and contributors paper 1 | Reference only; not integrated |
| MaveDB Link | https://github.com/berntpopp/mavedb-link authors and contributors paper 1 paper 2 | MCP: mavedb-link |
| MAVE-NN | https://github.com/jbkinney/mavenn authors and contributors paper 1 | Reference only; not integrated |
| Medea | https://github.com/mims-harvard/Medea authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MEGAHIT | https://github.com/voutcn/megahit authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Megalodon | https://github.com/nanoporetech/megalodon authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MEME Suite / FIMO | Charles E. Grant, Timothy L. Bailey, William S. Noble; MEME Suite contributors paper 1 | fimo-motifs |
| memesuite-lite | https://github.com/jmschrei/memesuite-lite authors and contributors paper 1 | Related local workflows: chipseq-motif-analysis, motif-search |
| Metagenomics Skills | PKU-EMBL项目作者与贡献者；Copyright (c) 2026 PKU-EMBL；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 paper 4 paper 5 paper 6 paper 7 paper 8 | 53 bundled Skills; Related local workflows: basalt, checkm2, metabat2, mgnify |
| MetaPhlAn | biobakery项目作者与贡献者 paper 1 paper 2 | Related local workflows: biobakery-databases, metagenomics-metaphlan, metagenomics-strain-tracking |
| metaWRAP | https://github.com/bxlab/metaWRAP authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| methplotlib | https://github.com/wdecoster/methplotlib authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MethylDackel | https://github.com/dpryan79/MethylDackel authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MethylGPT | albert-ying项目作者与贡献者；"Licensor" shall mean the copyright owner or entity authorized by；the copyright owner that is granting the License. paper 1 | Related local workflows: methylation-epigenetic-clocks |
| methylKit | al2na项目作者与贡献者 | Related local workflows: methylation-dmr-detection, methylation-methylkit |
| MGnify Genomes Catalogue Pipeline | EBI-Metagenomics项目作者与贡献者；Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/；(1) assert copyright on the software, and (2) offer you this License paper 1 | Related local workflows: mgnify, microbial-genome-characterization |
| MGnify MCP | MGS-sails项目作者与贡献者 | Related local workflows: mgnify |
| minfi | minfi authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| minigraph | lh3/minigraph authors and contributors paper 1 | minigraph-pangenome |
| Minigraph-Cactus | ComparativeGenomicsToolkit 项目及贡献者；论文作者见逐项原始引用 paper 1 | Related local workflows: comparative-genomics-pangenome-analysis, vitis-pangenome |
| Minimap2 | https://github.com/lh3/minimap2 authors and contributors; individual paper authors are not inferred supplied source 1 supplied source 2 | dnakit.annotation.genes.annotate_genes |
| miniprot | https://github.com/lh3/miniprot authors and contributors paper 1 | miniprot-align; Related local workflows: genome-annotation-annotation-transfer |
| mlst | https://github.com/tseemann/mlst authors and contributors; individual paper authors are not inferred | mlst-typing |
| MMseqs2 | https://github.com/soedinglab/MMseqs2 authors and contributors; individual paper authors are not inferred paper 1 | mmseqs-protein-search; mmseqs-protein-cluster |
| MMSplice / MTSplice | https://github.com/gagneurlab/MMSplice_MTSplice authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MoChA | https://github.com/freeseek/mocha authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Modkit | nanoporetech项目作者与贡献者；non-exclusive license under Contributor copyrights Licensable by such；Section 2.1 above, no copyright license is granted: | dnakit.genomics.read_bedmethyl; dnakit.genomics.summarize_methylation; modkit-pileup; Related local workflows: long-read-sequencing-nanopore-methylation, methylation-calling |
| moments | https://github.com/MomentsLD/moments authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MOODS | https://github.com/jhkorhonen/MOODS authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| mosdepth | brentp/mosdepth authors and contributors paper 1 | mosdepth-coverage |
| motifmatchr | motifmatchr authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| mOTUs | https://github.com/motu-tool/mOTUs authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MPRAflow | https://github.com/shendurelab/MPRAflow authors and contributors | Related local workflows: functional-screen-analysis |
| MrBayes | https://github.com/NBISweden/MrBayes authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MSMC2 | https://github.com/stschiff/msmc2 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| msprime | tskit-dev 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: population-genetics-scikit-allel-analysis |
| MToolBox | https://github.com/mitoNGS/MToolBox authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| MultiQC | https://github.com/MultiQC/MultiQC authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Multistrand | DNA-and-Natural-Algorithms-Group/multistrand authors and contributors paper 1 | Reference only; not integrated |
| MUSCLE | https://github.com/rcedgar/muscle authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.alignment.align_sequences |
| MutationalPatterns | https://github.com/UMCUGenetics/MutationalPatterns authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| NanoMethViz | https://github.com/Shians/NanoMethViz authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Nanopolish | https://github.com/jts/nanopolish authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| NCBI BLAST+ | NCBI BLAST+ authors and contributors; individual paper authors are not inferred supplied source 1 | dnakit.bioinformatics.alignment.build_blast_database; dnakit.bioinformatics.alignment.local_blast |
| NCBI Database MCP (hpend2373) | https://github.com/hpend2373/NCBI-Database-MCP authors and contributors; individual paper authors are not inferred | MCP: ncbi-database |
| NCBI Datasets | NCBI Datasets authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| NCBI EGAPx | https://github.com/ncbi/egapx authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Nextflow | https://github.com/nextflow-io/nextflow authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| nf-core/atacseq | nf-core/atacseq authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| nf-core/bacass | nf-core/bacass authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| nf-core/chipseq | nf-core/chipseq authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| nf-core/mag | nf-core/mag authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| nf-core/methylong | nf-core项目作者与贡献者；Copyright (c) The nf-core/methylong team；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 | Related local workflows: long-read-sequencing-nanopore-methylation |
| nf-core/methylseq | nf-core项目作者与贡献者；Copyright (c) The nf-core/methylseq team；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 | Related local workflows: methylation-bismark-alignment |
| nf-core/sarek | nf-core项目作者与贡献者；Copyright (c) The nf-core/sarek team；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 paper 4 | Related local workflows: nfcore-sarek-wrapper, workflows-fastq-to-variants |
| nf-core/taxprofiler | nf-core项目作者与贡献者；Copyright (c) The nf-core/taxprofiler team；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 paper 3 | Related local workflows: metagenomics-kraken, metagenomics-metaphlan |
| nf-core/eager | nf-core 项目及贡献者；论文作者见逐项原始引用 paper 1 | Related local workflows: grapevine-adna |
| NOREC4DNA | umr-ds/NOREC4DNA authors and contributors paper 1 | Reference only; not integrated |
| Nucleotide Transformer / AgroNT / SegmentNT | https://github.com/instadeepai/nucleotide-transformer authors and contributors; individual paper authors are not inferred supplied source 1 | dnakit.predictions.api.predict_sequence_properties; Related local workflows: nucleotide-transformer |
| Nuskell | DNA-and-Natural-Algorithms-Group/nuskell authors and contributors | Reference only; not integrated |
| OBITools4 | metabarcoding 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: ecological-genomics-edna-metabarcoding, workflows-edna-pipeline |
| ODGI | https://github.com/pangenome/odgi authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| OKseqHMM | https://github.com/CL-CHEN-Lab/OK-Seq authors and contributors paper 1 paper 2 paper 3 paper 4 paper 5 | Reference only; not integrated |
| Omics Skills | fmschulz项目作者与贡献者；Copyright (c) 2026 Frederik Schulz；The above copyright notice and this permission notice shall be included in all | 10 bundled Skills; Related local workflows: microbial-genome-characterization, viromics |
| OmicsClaw | TianGzlab/OmicsClaw authors and contributors | Reference only; not integrated |
| Open Targets MCP | https://github.com/nickzren/opentargets-mcp authors and contributors; individual paper authors are not inferred | MCP: opentargets |
| OpenCRAVAT | https://github.com/KarchinLab/open-cravat authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Operon | https://github.com/swaruplab/operon authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| OptiType | https://github.com/FRED-2/OptiType authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Orca | https://github.com/jzhoulab/orca authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| OrthoFinder | https://github.com/davidemms/OrthoFinder authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| oxDNA | lorenzo-rovigatti/oxDNA authors and contributors | Reference only; not integrated |
| pairtools | https://github.com/open2c/pairtools authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Panaroo | https://github.com/gtonkinhill/panaroo authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Pangolin splice predictor | https://github.com/tkzeng/Pangolin authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| pb-CpG-tools | https://github.com/PacificBiosciences/pb-CpG-tools authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| PCAngsd | https://github.com/Rosemeis/pcangsd authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Peppercorn | DNA-and-Natural-Algorithms-Group/peppercornenumerator authors and contributors | Reference only; not integrated |
| PGGB | pangenome 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: comparative-genomics-pangenome-analysis, vitis-pangenome |
| pgsc_calc | https://github.com/PGScatalog/pgsc_calc authors and contributors; individual paper authors are not inferred | Related local workflows: clinical-databases-polygenic-risk |
| PharmCAT | PharmGKB项目作者与贡献者；applicable copyright doctrines of fair use, fair dealing, or other；(including copyright notices, patent notices, disclaimers of warranty, paper 1 | Related local workflows: clinical-databases-pharmacogenomics, clinpgx |
| Piperine | DNA-and-Natural-Algorithms-Group/piperine authors and contributors | Reference only; not integrated |
| Plant Genomics MCP | https://github.com/musharna/plant-genomics-mcp authors and contributors; individual paper authors are not inferred | MCP: plant-genomics |
| PLINK 2 | chrchang/plink-ng authors and contributors | plink2-pca; plink2-king; plink2-ld-prune; plink2-gwas |
| polyRAD | Lindsay V. Clark, Alexander E. Lipka, Erik J. Sacks paper 1 | Related local workflows: polyploid-gene-family-cloning |
| PPanGGOLiN | https://github.com/labgem/PPanGGOLiN authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Precision Medicine MCP | https://github.com/lynnlangit/precision-medicine-mcp authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Predmoter | https://github.com/weberlab-hhu/Predmoter authors and contributors paper 1 paper 2 paper 3 paper 4 | Reference only; not integrated |
| PrimeDesign | https://github.com/pinellolab/PrimeDesign authors and contributors | Related local workflows: crispr-screens-prime-editing-screens |
| Primer3 | https://github.com/primer3-org/primer3 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| primer3-py | https://github.com/libnano/primer3-py authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ProCapNet | https://github.com/kundajelab/ProCapNet authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Prodigal | https://github.com/hyattpd/Prodigal authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| Prokka | tseemann/prokka authors and contributors paper 1 | prokka-annotation |
| PSMC | https://github.com/lh3/psmc authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| PubMed MCP (cyanheads) | https://github.com/cyanheads/pubmed-mcp-server authors and contributors; individual paper authors are not inferred | MCP: pubmed |
| PureCN | https://github.com/lima1/PureCN authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| pybedtools | https://github.com/daler/pybedtools authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| pyBigWig | https://github.com/deeptools/pyBigWig authors and contributors; individual paper authors are not inferred | Related local workflows: genome-intervals-bigwig-tracks |
| PyBrOpS | Robert Shrote and PyBrOpS contributors (MIT copyright); full paper author list at linked PMC article. paper 1 | Related local workflows: plant-genomics |
| pydna | https://github.com/pydna-group/pydna authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.cloning.assemble_duplexes; dnakit.bioinformatics.cloning.read_constructs |
| pyfaidx | https://github.com/mdshw5/pyfaidx authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| pyfastx | https://github.com/lmdu/pyfastx authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| PyPGx | https://github.com/sbslee/pypgx authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| PyRanges0 | https://github.com/pyranges/pyranges0 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Pyrodigal | https://github.com/althonos/pyrodigal authors and contributors paper 1 paper 2 | dnakit.genomics.predict_prokaryotic_genes; Related local workflows: genome-annotation-prokaryotic-annotation |
| pysam | https://github.com/pysam-developers/pysam authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.reads.alignment_summary; dnakit.bioinformatics.reads.coverage_consensus |
| pySBOL3 | https://github.com/SynBioDex/pySBOL3 authors and contributors paper 1 | Reference only; not integrated |
| QIIME2 / Rachis framework | https://github.com/rachis-org/rachis authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| QUAST | https://github.com/ablab/quast authors and contributors; individual paper authors are not inferred paper 1 | quast-assembly |
| R/qtl | R/qtl authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| R/qtl2 | R/qtl2 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| RAxML-NG | amkozlov 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: phylo-modern-tree-inference |
| REGENIE | https://github.com/rgcgithub/regenie authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Remora | https://github.com/nanoporetech/remora authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| RepeatMasker | https://github.com/Dfam-consortium/RepeatMasker authors and contributors; individual paper authors are not inferred | repeatmasker-library |
| RepeatModeler | https://github.com/Dfam-consortium/RepeatModeler authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| ResFinder | https://github.com/genomicepidemiology/resfinder authors and contributors; individual paper authors are not inferred | Related local workflows: disinfinder |
| RFMix | slowkoni 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: ancestry-risk-profiler, population-genetics-population-structure |
| RGI | https://github.com/arpcard/rgi authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| rMVP | https://github.com/xiaolei-lab/rMVP authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| rrBLUP | Jeffrey B. Endelman paper 1 paper 2 paper 3 | dnakit.genomics.genomic_prediction; Related local workflows: workflows-gwas-pipeline; Independent fixed-lambda ridge implementation; does not call R rrBLUP or estimate REML. |
| Rsamtools | Rsamtools authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Rule Set 3 | https://github.com/gpp-rnd/rs3 authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SAIGE | https://github.com/saigegit/SAIGE authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SAMtools | https://github.com/samtools/samtools authors and contributors; individual paper authors are not inferred | dnakit.bioinformatics.ngs.prepare_bam; Related local workflows: cite-encode, samtools-bam-processing |
| scadnano | UC-Davis-molecular-computing/scadnano-python-package authors and contributors paper 1 | dnakit.genomics.design_dna_duplex; dnakit.genomics.export_oxdna_design; Related local workflows: dnakit-dna-nanotechnology |
| scarHRD | https://github.com/sztup/scarHRD authors and contributors paper 1 | Reference only; not integrated |
| SCENIC+ | https://github.com/aertslab/scenicplus authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| schmutzi | grenaud 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: grapevine-adna |
| scikit-allel | https://github.com/cggh/scikit-allel authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Sei | https://github.com/FunctionLab/sei-framework authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SemiBin | https://github.com/BigDataBiology/SemiBin authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SeqKit | shenwei356项目作者与贡献者；Copyright © 2016-2019 Wei Shen, 2019 Oxford Nanopore Technologies.；The above copyright notice and this permission notice shall be included in paper 1 | Related local workflows: read-sequences |
| seqtk | https://github.com/lh3/seqtk authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SeSAMe | SeSAMe authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Signac | https://github.com/stuart-lab/signac authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SigProfilerAssignment | https://github.com/SigProfilerSuite/SigProfilerAssignment authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SigProfilerExtractor | AlexandrovLab项目作者与贡献者；Copyright (c) 2019, S M Ashiqul Islam (Mishu) [Alexandrov Lab]；1. Redistributions of source code must retain the above copyright notice, this paper 1 | Related local workflows: clinical-databases-somatic-signatures |
| SigProfilerMatrixGenerator | https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SimBiology MCP | https://github.com/Sepanta-Yalameha/SIMBIOLOGY-MCP authors and contributors | Reference only; not integrated |
| SLiM | Benjamin C. Haller (copyright) and MesserLab/SLiM contributors; use version-specific citation from SLiM manual. | Related local workflows: ecological-genomics-conservation-genetics |
| SMC++ | https://github.com/popgenmethods/smcpp authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Snakemake | https://github.com/snakemake/snakemake authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SnapATAC2 | scverse项目作者与贡献者；Copyright (c) 2022-2026 Kai Zhang；The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. paper 1 | Related local workflows: atac-seq-single-cell-atac |
| Sniffles2 | fritzsedlazeck项目作者与贡献者；Copyright (c)；The above copyright notice and this permission notice shall be included in all paper 1 paper 2 | sniffles-sv; Related local workflows: long-read-sequencing-structural-variants, variant-calling-structural-variant-calling |
| Snippy | https://github.com/tseemann/snippy authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SnpEff / SnpSift | https://github.com/pcingola/SnpEff authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| sommer | Giovanny Covarrubias-Pazaran paper 1 | Related local workflows: causal-genomics-heritability-partitioning |
| SPAdes | ablab项目作者与贡献者；Copyright (c) 2023-2024 SPAdes team；Copyright (c) 2015-2022 Saint Petersburg State University paper 1 | dnakit.bioinformatics.ngs.assemble_reads; Related local workflows: genome-assembly-short-read-assembly |
| SpliceAI | https://github.com/Illumina/SpliceAI authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Statistical Genetics Skills | svdorn/statgen-skills authors and contributors | 10 bundled Skills |
| stdpopsim | https://github.com/popsim-consortium/stdpopsim authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Straglr | https://github.com/BirolLab/straglr authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| STRait Razor | Ahhgust 项目及贡献者；论文作者见逐项原始引用 | Related local workflows: variant-calling |
| Strelka2 | https://github.com/Illumina/strelka authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| STRling | https://github.com/quinlan-lab/STRling authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| susieR | https://github.com/stephenslab/susieR authors and contributors; individual paper authors are not inferred supplied source 1 supplied source 2 | Reference only; not integrated |
| SVIM | https://github.com/eldariont/svim authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| SynBioHub | https://github.com/SynBioHub/synbiohub authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| tangermeme | https://github.com/jmschrei/tangermeme authors and contributors paper 1 | 1 bundled Skills |
| TASSEL | TASSEL authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Telomerecat | https://github.com/cancerit/telomerecat authors and contributors | Reference only; not integrated |
| TelomereHunter2 | https://github.com/ferdinand-popp/telomerehunter2 authors and contributors paper 1 paper 2 paper 3 | Reference only; not integrated |
| TF-MoDISco | https://github.com/kundajelab/tfmodisco authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| TOBIAS | https://github.com/loosolab/TOBIAS authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Tombo | https://github.com/nanoporetech/tombo authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Trim Galore | https://github.com/FelixKrueger/TrimGalore authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| TRTools | https://github.com/gymrek-lab/TRTools authors and contributors; individual paper authors are not inferred supplied source 1 | Reference only; not integrated |
| Truvari | https://github.com/ACEnglish/truvari authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| tskit | https://github.com/tskit-dev/tskit authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| TwoSampleMR | https://github.com/MRCIEU/TwoSampleMR authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| TxAgent | https://github.com/mims-harvard/TxAgent authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| UCSC Genome MCP | https://github.com/hlydecker/ucsc-genome-mcp authors and contributors; individual paper authors are not inferred | MCP: ucsc-genome |
| UNACORM | AAnzel/UNACORM authors and contributors paper 1 | Reference only; not integrated |
| Unicycler | https://github.com/rrwick/Unicycler authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| updog | David Gerard, Luís Felipe Ventorim Ferrão, Antonio Augusto Franco Garcia, Matthew Stephens paper 1 | Related local workflows: polyploid-gene-family-cloning |
| VAMB | https://github.com/RasmussenLab/vamb authors and contributors; individual paper authors are not inferred | Related local workflows: taxvamb |
| VanRaden genomic relationship method 1 | Paul M. VanRaden paper 1 | dnakit.genomics.genomic_relationship_matrix |
| VariantAnnotation | VariantAnnotation authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Bioinformatics Agent Skills | variomeanalytics/bioinformatics-agent-skills authors and contributors | Reference only; not integrated |
| vg | https://github.com/vgteam/vg authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| VSEARCH | https://github.com/torognes/vsearch authors and contributors; individual paper authors are not inferred paper 1 | vsearch-dereplicate; vsearch-cluster |
| WhatsHap | https://github.com/whatshap/whatshap authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
| Winnowmap | https://github.com/marbl/Winnowmap authors and contributors; individual paper authors are not inferred | Reference only; not integrated |
4) How to inspect evidence and dependencies¶
from dnakit.integrations import search_projects, describe_analysis
print(search_projects('BOLE'))
print(search_projects(domain='dna-storage'))
print(describe_analysis('plink2-pca'))
The packaged search returns primary links, license evidence, local skill matches, gaps and actual adapter IDs. The source repository stores the search log in registry/genomics-survey.json and its research parts. Use dnakit skills cite SKILL_ID for pinned workflow attribution. External software/model/data terms apply separately.