Process SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ genomic files via htslib.
npx skills add https://github.com/sanand0/scientific-research --skill pysam-sanand0
Please help me install this Agent Skill. Skill: pysam Source: https://github.com/sanand0/scientific-research/tree/main/.claude/skills/pysam Command: npx skills add https://github.com/sanand0/scientific-research --skill pysam-sanand0
This Skill provides a powerful Python interface for efficiently reading, manipulating, and writing complex genomic data files, streamlining bioinformatics workflows.
Use the pysam skill to read the first 1000 bases from chromosome 1 in the 'reference.fasta' file.
High-intent search queries and answers about installing and using this skill.
You can read, filter, and manipulate VCF/BCF variant files in Python by using a htslib-based interface designed for NGS analysis. This provides a Pythonic way to parse variant calls and extract data like quality scores and allele frequency directly.
Yes, extracting specific genomic regions from SAM/BAM/CRAM alignments is supported through region-based querying. This allows you to target specific chromosome coordinates directly in Python to calculate coverage or perform pileup analysis.
FASTA and FASTQ sequence manipulation is fully supported for NGS data processing. You can efficiently read, write, and extract reference sequences to integrate them into genomic analysis workflows alongside alignment and variant data.
Performing pileup analysis on genomic alignments is best handled by using a Pythonic interface to the htslib library. This enables efficient calculation of base coverage and extraction of alignment data across specific genomic regions.
To filter variant calls based on allele frequency from a VCF file, you can parse the variants using a Pythonic htslib interface. This allows you to apply custom filters to quality scores and allele frequencies, then extract corresponding reference sequences from a FASTA file for further investigation.
jaechang-hitsTrim adapters and filter quality in FASTQ files using fastp.
Zeyuyang-0420Read, manipulate, and analyze genomic datasets in SAM/BAM/CRAM and VCF/BCF formats.
RamanEbrahimiProcess genomic alignment, variant, and sequence files for NGS analysis.
galeepProvide Pythonic interfaces for SAM/BAM/CRAM and VCF/BCF genomic file operations.
