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Pysam

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davila7·vlatest·backend·MIT

Pysam allows you to efficiently manipulate and analyze large genomic datasets by providing Python bindings for the popular pysam library.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add davila7/claude-code-templates --skill pysam -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

davila7

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Install target

Live repository

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About this skill

What it does

This skill provides access to the pysam library, a Python package for working with SAM/BAM files. It allows you to parse and manipulate sequence alignment data, extract genomic coordinates from alignments, and perform various analyses on aligned reads. This is particularly useful for bioinformatics tasks involving next-generation sequencing data.

When to use it

  • Analyzing RNA-Seq data: Extract read counts for genes or regions of interest.
  • Variant calling: Identify potential genetic variants based on alignment discrepancies.
  • Genome annotation: Process and analyze genomic annotations from BAM files.
  • Quality control: Assess the quality of sequencing reads by examining alignment statistics.

Key capabilities

  • SAM/BAM file parsing
  • Sequence alignment data manipulation
  • Genomic coordinate extraction
  • Alignment statistics analysis

Example prompts

  • "Extract the number of reads aligned to gene 'BRCA1' from this BAM file."
  • "Give me a list of all variants with a mapping quality below 20 in this BAM file."
  • "Calculate the average insert size for paired-end reads in this BAM file."

Tips & gotchas

Requires familiarity with bioinformatics concepts and SAM/BAM file formats. The skill's output will be based on the data within the provided input files, so ensure those files are accessible and correctly formatted.