Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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

• Updated Jul 25, 2026
• C

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

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

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

lang-python status-archived domain-bioinformatics interface-cli method-deep-learning role-application interface-api status-published scope-focused domain-drug-discovery method-language-model task-sequence-analysis entity-sequence

• Updated Jul 25, 2024
• Python

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++

The second version of the Kraken taxonomic sequence classification system

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

• Updated Jul 29, 2026
• C++

Official git repository for Biopython (originally converted from CVS)

status-active lang-python domain-bioinformatics task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence ecosystem-biopython

• Updated Jul 28, 2026
• Python

C library for high-throughput sequencing data formats

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

• Updated Jul 28, 2026
• C

status-active lang-python domain-bioinformatics interface-cli method-deep-learning role-framework domain-structural-biology entity-protein interface-api status-published scope-swissknife method-language-model task-sequence-analysis entity-sequence task-structure-prediction task-protein-design

• Updated Jul 28, 2026
• Jupyter Notebook

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++

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

IQ-TREE software version 2: phylogenetics by maximum likelihood

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

• Updated Jul 22, 2026
• C++

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

A comprehensive library for computational molecular biology

status-active lang-python domain-bioinformatics domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence

• Updated Jul 21, 2026
• Python

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

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

Single-cell analysis in Python. Scales to >100M cells.

status-active lang-python task-visualization domain-bioinformatics task-file-io interface-api status-published status-packaged-pypi status-packaged-conda method-machine-learning method-statistics role-toolkit scope-swissknife task-sequence-analysis entity-sequence domain-single-cell entity-multi-omics ecosystem-scverse

• Updated Jul 28, 2026
• Python

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

• Updated May 19, 2026
• C

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

status-active lang-python task-alignment domain-bioinformatics task-file-io entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence

• Updated Jul 28, 2026
• Python