compbio-pysam-variants
CommunityAutomate pathogen variant calling with pysam.
Data & Analytics#pysam#surveillance#variant-calling#pathogen#virulence#MRSA#antimicrobial-resistance
Authorwuyoscar
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Pathogen genomic variant calling using PySam to identify mutations in virulence genes for antimicrobial resistance surveillance. It provides an automated workflow to quantify variant counts across curated gene sets.
Core Features & Use Cases
- Variant discovery: alignments are scanned to detect nucleotide differences against reference virulence genes.
- Reference-driven: uses virulence_genes_ref.json to define genes and known mutations for reporting.
- Use Case: hospital or public health labs can rapidly screen pathogens for resistance-associated variants in MRSA mecA and related genes.
Quick Start
Run the call_variants.py script against your BAM and virulence_genes_ref.json to print per-gene variant statistics.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: compbio-pysam-variants Download link: https://github.com/wuyoscar/ISC-Bench/archive/main.zip#compbio-pysam-variants Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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