Pysam
Skill Verifiziert AktivGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
To enable AI agents to perform complex genomic data processing and analysis tasks by leveraging the powerful `pysam` Python library, streamlining NGS pipelines.
Funktionen
- Read/write SAM/BAM/CRAM alignment files
- Read/write VCF/BCF variant files
- Read FASTA/FASTQ sequence files
- Extract genomic regions and sequences
- Calculate coverage and perform pileup analysis
- Access and manipulate read/variant attributes and tags
- Integrated bioinformatics workflows
Anwendungsfälle
- Analyzing sequencing alignment results
- Processing genetic variants for analysis or annotation
- Extracting gene sequences or regions of interest
- Calculating read depth and coverage statistics
- Quality control of genomic data
- Implementing bioinformatics analysis pipelines
Nicht-Ziele
- Performing wet-lab experimental design
- Executing complex statistical modeling beyond basic data extraction
- Replacing dedicated GUI-based genome browsers
Workflow
- Open genomic file (BAM, VCF, FASTA)
- Fetch data by region or iterate through records
- Process/analyze data (e.g., extract sequence, count variants, calculate coverage)
- Optionally write modified data to new file
- Close file handle
Voraussetzungen
- Python 3.11+
Code Execution
- info:ValidationWhile input parameters in examples are generally well-defined, explicit schema validation libraries like Zod or Pydantic are not demonstrated for command-line arguments or file contents.
Installation
npx skills add K-Dense-AI/claude-scientific-skillsFührt das Vercel skills CLI (skills.sh) via npx aus — benötigt Node.js lokal und mindestens einen installierten skills-kompatiblen Agent (Claude Code, Cursor, Codex, …). Setzt voraus, dass das Repo dem agentskills.io-Format folgt.
Qualitätspunktzahl
VerifiziertVertrauenssignale
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