{"categories":[{"label":"Software Development","url":"https://skillfed.io/packages/category/software-development/5"},{"label":"Scientific/Engineering","url":"https://skillfed.io/packages/category/scientific-engineering/3"}],"enrichment":{"capability":"pysam reads, manipulates, and writes genomic data files (SAM/BAM/CRAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ) and provides access to samtools and bcftools command-line functionality through a Python wrapper around HTSlib.","skillfed_tags":["bioinformatics","genomics","htSlib-wrapper"],"use_cases":["Parse and filter SAM/BAM files in a genomic analysis pipeline without calling samtools as a subprocess","Extract specific genomic regions or read alignments from indexed VCF/BCF files for variant analysis","Convert between genomic file formats (e.g., BAM to CRAM) programmatically within a Python workflow","Access samtools and bcftools functionality directly from Python without shell subprocess overhead","Build custom bioinformatics tools that need to read FASTA/FASTQ sequences and alignment data"],"what_it_does":"pysam is a Python wrapper around HTSlib, the C library underlying samtools and bcftools, that lets you read and write genomic sequence data in standard formats (SAM, BAM, CRAM, VCF, BCF, BED, GFF, GTF, FASTA, FASTQ). It provides both low-level access to HTSlib's C API via Cython and a high-level Python interface for working with genomic data, including support for compression and random access through indexing.\n\nThe package is widely used in bioinformatics pipelines and genomic analysis workflows. It has no runtime dependencies beyond HTSlib itself (bundled in the wheel), making it straightforward to integrate into data processing scripts. Active maintenance and broad platform support (macOS, Linux) with prebuilt wheels for Python 3.10\u20133.13 mean installation is typically frictionless on supported systems.","worth_installing":"Yes. pysam is actively maintained, has no runtime dependencies, carries a permissive MIT license, and is essential for any Python-based genomic data processing. Medium install friction is offset by prebuilt wheels for modern Python versions and the absence of external runtime requirements. No known vulnerabilities."},"id":"pysam","links":{"html":"https://skillfed.io/packages/pysam","md":"https://skillfed.io/packages/pysam.md","pypi":"https://pypi.org/project/pysam/"},"maintenance":{"status":"active"},"meta":{"latest_release":"2026-04-27","license_spdx":null,"license_treatment":"permissive","name":"pysam","python_support":"supports_current","summary":"Package for reading, manipulating, and writing genomic data"},"popularity":{"monthly_downloads":1291977,"position":4103,"tier":"top_5000"},"security":{"n_vulnerabilities":0},"version":"0.24.0"}