Library
pysam agent skills for Claude Code, Codex and other agents.
- skills
- 22
- Type
- Library
- Website
- pysam.readthedocs.io
- Official GitHub
- pysam-developers
pysam skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Soft- or hard-clips PCR primer footprints from aligned amplicon BAMs so primer bases stop masquerading as confirmed reference sequence. | GPTomics/ | 1.2k | 2 repos | ~2.2k | Automated safety check: Pass | MIT | 1 mo ago |
| 2 | Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. | GPTomics/ | 1.2k | 2 repos | ~2.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 3 | 3.Pysam Genomic file toolkit. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 11 repos | ~2.5k | Automated safety check: Pass | MIT | today |
| 4 | Sort alignment files by coordinate or read name using samtools and pysam. | GPTomics/ | 1.2k | 2 repos | ~2.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 5 | 5.Pysam Provides Python/HTSlib workflows for genomic files. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~3.4k | Automated safety check: Notes | MIT | 3 days ago |
| 6 | Omics and single-cell workflow guide for AnnData, Scanpy-style dataset profiling, PyDESeq2-oriented count checks, pysam alignment inspection, and pyOpenMS mass-spectrometry summaries. | DrugClaw/ | 125 | — | ~1.1k | Automated safety check: Pass | Apache-2.0 | 6 mo ago |
| 7 | Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. | GPTomics/ | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 8 | Annotate copy number variant segments with overlapping genes, dosage-sensitivity scores, cancer driver databases, population frequencies, and clinical-variant content. | GPTomics/ | 1.2k | 2 repos | ~3.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 9 | Mark and remove PCR/optical duplicates using samtools fixmate and markdup. | GPTomics/ | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 10 | Generate consensus sequences and manage reference files using samtools. | GPTomics/ | 1.2k | 2 repos | ~3.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 11 | View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. | GPTomics/ | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 12 | Production-ready genomics and epigenomics data processing for BixBench questions. | wu-yc/ | 1.1k | 2 repos | ~14k | Automated safety check: Pass | No licence | 6 mo ago |
| 13 | Filter alignments by flags, mapping quality, and regions using samtools view and pysam. | majiayu000/ | 666 | 3 repos | ~1.9k | Automated safety check: Pass | MIT | yesterday |
| 14 | Generate pileup data for variant calling using samtools mpileup and pysam. | majiayu000/ | 666 | 3 repos | ~2.2k | Automated safety check: Pass | MIT | yesterday |
| 15 | Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx. | GPTomics/ | 1.2k | 1 repo | ~3k | Automated safety check: Pass | MIT | 1 mo ago |
| 16 | Detects somatic mutations in circulating tumor DNA, treating low-VAF detection as a signal-versus-noise problem set by error suppression and molecules sampled, not by the choice of caller. | GPTomics/ | 1.2k | 1 repo | ~5.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 17 | ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate… | FreedomIntelligence/ | 3.1k | — | ~2.7k | Automated safety check: Pass | No licence | 2 mo ago |
| 18 | Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC. | FreedomIntelligence/ | 3.1k | — | ~1.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 19 | Biopython sequence analysis: parse FASTA/FASTQ/GenBank/GFF (SeqIO), NCBI Entrez (esearch/efetch/elink), remote/local BLAST, pairwise/MSA alignment (PairwiseAligner, MUSCLE/ClustalW), phylogenetic… | jaechang-hits/ | 370 | 1 repo | ~8.5k | Automated safety check: Pass | BSD-3-Clause | 9 days ago |
| 20 | CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. | jaechang-hits/ | 370 | 1 repo | ~4.1k | Automated safety check: Pass | MIT | 9 days ago |
| 21 | 21.Pysam Genomic file toolkit. An agent skill from aipoch/medical-research-skills. | aipoch/ | 2k | — | ~3.4k | Automated safety check: Pass | MIT | 21 days ago |
| 22 | Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. An agent skill from jaechang-hits/SciAgent-Skills. | jaechang-hits/ | 370 | 1 repo | ~5.2k | Automated safety check: Pass | MIT | 9 days ago |
Questions, answered from the data.
What is the best pysam skill?
Amplicon Primer Clipping from GPTomics/bioSkills ranks first of the 22 pysam skills listed here, with the highest score: its repository has 1.2k GitHub stars, 2 other GitHub owners carry a copy, its SKILL.md loads about 2.2k tokens and it passes the automated safety check with no findings. Next come Bio Alignment Indexing and Pysam.
Is there an official pysam skill?
None yet. All 22 pysam skills listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.