# One-time use (no install required)
npx bioskill install
# Or install globally for repeated use
npm install -g bioskill
bioskill install
Awesome Bio Agent Skills
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
1,676 deduplicated skills from 20 open-source repositories, organized into 15 categories. Each skill is a self-contained SKILL.md folder compatible with Claude-based agent frameworks (OpenClaw, NanoClaw, Biomni).
Contents
- Genomics
- Proteomics
- Single-Cell Analysis
- Biology and AI
- Clinical and Medical
- Transcriptomics
- Database Query
- Multi-Omics Integration
- Bioinformatics Utilities
- Visualization
- Workflow Orchestration
- Epigenomics
- Pathway Analysis
- Metagenomics
- Protein Design
- Sources
Genomics
526 skills — WGS/WES analysis, variant annotation, GWAS, CNV, structural variants, haplotype phasing, genome assembly.
| Skill | Source | Description |
|---|---|---|
| bio-alignment-amplicon-clipping | bioskills | Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer pan... |
| bio-alignment-filtering | bioskills | Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality al... |
| bio-alignment-indexing | bioskills | Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific... |
| bio-alignment-io | bioskills | Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and othe... |
| bio-alignment-msa-parsing | bioskills | Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations,... |
| bio-alignment-msa-statistics | bioskills | Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing... |
| bio-alignment-multiple | bioskills | Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, seq... |
| bio-alignment-pairwise | bioskills | Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scorin... |
| bio-alignment-sorting | bioskills | Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end... |
| bio-alignment-structural | bioskills | Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coor... |
| bio-alignment-trimming | bioskills | Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when re... |
| bio-alignment-validation | bioskills | Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when... |
| bio-atac-seq-allele-specific-accessibility | bioskills | Detect allele-specific chromatin accessibility from ATAC-seq using WASP, GATK ASEReadCounter, or RASQUAL. Use when mapping cis-regulatory genetic v... |
| bio-atac-seq-atac-peak-calling | bioskills | Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligne... |
| bio-atac-seq-consensus-peakset | bioskills | Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and major... |
| bio-bam-statistics | bioskills | Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating cove... |
| bio-basecalling | bioskills | Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified b... |
| bio-bedgraph-handling | bioskills | Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization,... |
| bio-biomart-queries | bioskills | Bulk-query Ensembl BioMart (and other BioMart instances) for cross-database ID mapping, gene/transcript/exon coordinates, and ortholog tables. Use... |
| bio-causal-genomics-colocalization-analysis | bioskills | Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR,... |
| bio-causal-genomics-effector-gene-prioritization | bioskills | Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021),... |
| bio-causal-genomics-fine-mapping | bioskills | Resolves GWAS associations to candidate causal variants and credible sets via SuSiE, susie_rss, FINEMAP, CAVIAR, DAP-G, PAINTOR, PolyFun, SuSiEx, M... |
| bio-causal-genomics-genetic-correlation | bioskills | Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL,... |
| bio-causal-genomics-genomic-sem | bioskills | Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor... |
| bio-causal-genomics-mediation-analysis | bioskills | Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-st... |
| bio-causal-genomics-mendelian-randomization | bioskills | Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egge... |
| bio-causal-genomics-pleiotropy-detection | bioskills | Detect and adjust for horizontal pleiotropy in two-sample Mendelian randomization by distinguishing uncorrelated (UHP) from correlated (CHP) pleiot... |
| bio-causal-genomics-proteome-mr-drug-target | bioskills | Runs cis-pQTL Mendelian randomization for drug-target validation using UKB-PPP (Olink), deCODE (SomaScan), Fenland, INTERVAL, ARIC, and FinnGen-PPP... |
| bio-causal-genomics-transcriptome-wide-association | bioskills | P |