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pysam-developers avatar

pysam-developers/pysam

0
View on GitHub↗
895 stars·298 forks·Cython·MIT·12 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.

Star history

Star history chart for pysam-developers/pysamStar history chart for pysam-developers/pysam

How this analysis was created: This summary and feature list are AI-generated from collected project material and can contain mistakes. Stars, license and language are imported from GitHub. Inclusion does not mean that we have tested or audited this project. Check the source documentation for any feature you depend on. Learn more on our About page.

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Projects sharing features with Pysam

These projects share indexed features with Pysam. Shared tags can include platform or build tooling; verify the primary use case before treating a result as a replacement.
  • biodatageeks/polars-biobiodatageeks avatar

    biodatageeks/polars-bio

    168View on GitHub↗

    Blazing-Fast Bioinformatic Operations on Python DataFrames

    Python
    View on GitHub↗168
  • brentp/cruzdbbrentp avatar

    brentp/cruzdb

    137View on GitHub↗

    python access to UCSC genomes database

    Python
    View on GitHub↗137
  • brentp/cyvcf2brentp avatar

    brentp/cyvcf2

    445View on GitHub↗

    cython htslib == fast VCF and BCF processing

    Cython
    View on GitHub↗445
  • arq5x/cyvcfarq5x avatar

    arq5x/cyvcf

    53View on GitHub↗

    A fast Python library for VCF files leveraging Cython for speed.

    Python
    View on GitHub↗53
Compare all 10 related projects→

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.

Which projects share features with pysam-developers/pysam?

Projects with overlapping indexed features 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").