Is an index file required for all operations?

Index files (like .bai, .fai, or .tbi) are required for random access to specific genomic regions, but sequential reading can be performed using fetch(until_eof=True).

Can I run samtools commands directly with this skill?

Yes, the skill includes wrappers for samtools and bcftools, allowing you to sort, index, and view files directly from Python code.

What genomic file formats does the Pysam skill support?

It supports SAM, BAM, and CRAM for alignments; VCF and BCF for variants; and FASTA and FASTQ for sequences.

Does Pysam use 0-based or 1-based coordinates?

Pysam follows Python convention using 0-based, half-open coordinates, though it can handle 1-based string queries via samtools.

Pysam Genomic Data Toolkit

Name: Pysam Genomic Data Toolkit
Author: BbgnsurfTech

byBbgnsurfTech

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Data Science & ML

Processes and analyzes genomic data formats including BAM, VCF, and FASTA using a Pythonic interface to htslib.

About

Pysam is a specialized Claude Code skill designed for bioinformatics workflows, providing high-performance access to genomic datasets through the htslib library. It enables seamless reading, writing, and manipulation of common sequencing formats such as SAM/BAM/CRAM alignments, VCF/BCF variant records, and FASTA/FASTQ reference sequences. This skill is particularly useful for building NGS data processing pipelines, calculating read coverage via pileup analysis, and performing region-based queries on indexed genomic files, all while adhering to Pythonic 0-based coordinate conventions.

Key Features

Random access to indexed FASTA and FASTQ sequences
Integrated wrappers for samtools and bcftools commands
Read and write SAM/BAM/CRAM alignment files
Process VCF/BCF variant files and genotype data
Calculate genomic coverage and perform pileup analysis
3 GitHub stars

Use Cases

Extracting specific genomic regions for downstream statistical analysis
Developing automated NGS bioinformatics analysis pipelines
Performing variant annotation and quality control on sequencing data

About

Key Features

Random access to indexed FASTA and FASTQ sequences
Integrated wrappers for samtools and bcftools commands
Read and write SAM/BAM/CRAM alignment files
Process VCF/BCF variant files and genotype data
Calculate genomic coverage and perform pileup analysis
3 GitHub stars

Use Cases

Extracting specific genomic regions for downstream statistical analysis
Developing automated NGS bioinformatics analysis pipelines
Performing variant annotation and quality control on sequencing data