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pysam-developers avatar

pysam-developers/pysam

0
View on GitHub↗
895 stars·298 forks·Cython·MIT·5 viewspysam.readthedocs.io/en/latest↗

Pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

Features

  • Python Bioinformatics Modules - Python wrapper for SAM/BAM file manipulation tools.

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Open-source alternatives to Pysam

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  • arq5x/cyvcfarq5x avatar

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Frequently asked questions

What does pysam-developers/pysam do?

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

What are the main features of pysam-developers/pysam?

The main features of pysam-developers/pysam are: Python Bioinformatics Modules.

What are some open-source alternatives to pysam-developers/pysam?

Open-source alternatives to pysam-developers/pysam include: arq5x/cyvcf — A fast Python library for VCF files leveraging Cython for speed. biodatageeks/polars-bio — Blazing-Fast Bioinformatic Operations on Python DataFrames. brentp/cruzdb — python access to UCSC genomes database. brentp/cyvcf2 — cython + htslib == fast VCF and BCF processing. cokelaer/bioservices — Access to Biological Web Services from Python. daler/pybedtools — Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic").