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.

status-active role-library lang-python lang-c domain-bioinformatics task-file-io method-chemoinformatics interface-api status-published status-packaged-pypi status-packaged-conda scope-focused entity-nucleic-acid entity-sequence domain-genomics

Updated Jul 19, 2026
Cython

Scindices / instadeepai--nucleotide-transformer

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Foundation Models for Genomics & Transcriptomics

status-active lang-python domain-bioinformatics method-deep-learning role-framework interface-api interface-jupyter status-published scope-focused entity-nucleic-acid method-language-model task-sequence-analysis entity-sequence domain-genomics

Updated Feb 24, 2026
Jupyter Notebook

Scindices / Ensembl--ensembl-vep

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The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

status-active lang-python lang-perl domain-bioinformatics interface-cli role-application status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid entity-sequence method-rule-based domain-genomics task-variant-analysis

Updated Jul 24, 2026
Perl

Scindices / google--deepvariant

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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

status-active lang-python lang-cpp domain-bioinformatics interface-cli method-deep-learning role-application status-published scope-focused entity-nucleic-acid entity-sequence interface-gpu domain-genomics task-variant-analysis

Updated Mar 19, 2026
Python

Scindices / lh3--minimap2

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A versatile pairwise aligner for genomic and spliced nucleotide sequences

Updated May 19, 2026
C

Scindices / arq5x--bedtools2

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bedtools - the swiss army knife for genome arithmetic

status-active lang-cpp lang-c domain-bioinformatics interface-cli role-application task-file-io status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jun 10, 2026
C

Scindices / broadinstitute--gatk

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Official code repository for GATK versions 4 and up

status-active lang-java lang-python domain-bioinformatics interface-cli task-workflow task-file-io status-published method-machine-learning method-statistics role-toolkit scope-swissknife entity-nucleic-acid entity-sequence domain-genomics task-variant-analysis

Updated Jul 30, 2026
Java

Scindices / seqan--seqan3

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The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

status-active task-alignment lang-cpp domain-bioinformatics task-file-io interface-api status-published method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jul 20, 2026
C++

Scindices / nanoporetech--dorado

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Oxford Nanopore's Basecaller

status-active lang-python lang-cpp domain-bioinformatics interface-cli method-deep-learning role-application status-published status-packaged-conda scope-focused entity-nucleic-acid task-sequence-analysis entity-sequence interface-gpu domain-genomics

Updated Jul 22, 2026
C++

Scindices / samtools--samtools

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Tools (written in C using htslib) for manipulating next-generation sequencing data

status-active task-alignment lang-c domain-bioinformatics interface-cli role-application task-file-io method-chemoinformatics status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid entity-sequence domain-genomics

Updated Jul 28, 2026
C

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