Does this skill handle genomic coordinate systems?

Yes, Pysam uses 0-based, half-open coordinates (standard Python convention), but also handles the 1-based strings used in samtools fetch operations.

Are index files required for all operations?

Random access to specific regions requires index files (like .bai for BAM or .tbi for VCF), though you can read files sequentially without them using the until_eof parameter.

Can I use samtools commands with this skill?

Yes, Pysam provides a Python interface to many samtools and bcftools commands, allowing you to sort, index, and view files programmatically.

What genomic file formats does Pysam support?

Pysam supports common high-throughput sequencing formats including SAM, BAM, and CRAM for alignments; VCF and BCF for variants; and FASTA and FASTQ for sequences.

Pysam Genomic Toolkit

Name: Pysam Genomic Toolkit
Author: pur3v4d3r

bypur3v4d3r

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데이터 과학 및 ML

Processes and analyzes genomic datasets including SAM, BAM, VCF, and FASTA files using a Pythonic interface to htslib.

소개

Pysam is a comprehensive Python module designed for the manipulation of high-throughput sequencing data. It provides a robust interface for reading, writing, and querying standard genomic file formats like SAM/BAM/CRAM alignments and VCF/BCF variants, making it an essential tool for bioinformaticians. Whether you are performing pileup analysis for coverage, extracting specific genomic regions, or building complex data processing pipelines, this skill provides the patterns and guidance needed to integrate NGS data handling directly into your Claude-assisted development workflow.

주요 기능

1 GitHub stars
High-performance region-based querying for indexed genomic files.
Built-in pileup analysis for calculating sequence coverage and depth.
Native handling of 0-based coordinate systems and htslib functionality.
Integrated access to samtools and bcftools command-line utilities.
Read/write support for SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ formats.

사용 사례

Developing bioinformatics pipelines for NGS data processing and quality control.
Extracting specific genomic regions or variants for downstream analysis.
Automating variant calling, annotation, and genotype filtering workflows.

소개

주요 기능

1 GitHub stars
High-performance region-based querying for indexed genomic files.
Built-in pileup analysis for calculating sequence coverage and depth.
Native handling of 0-based coordinate systems and htslib functionality.
Integrated access to samtools and bcftools command-line utilities.
Read/write support for SAM, BAM, CRAM, VCF, BCF, FASTA, and FASTQ formats.

사용 사례

Developing bioinformatics pipelines for NGS data processing and quality control.
Extracting specific genomic regions or variants for downstream analysis.
Automating variant calling, annotation, and genotype filtering workflows.