Open-Source Bioinformatics Tool List

Genomic bioinformatics tools

Open-source software for next-generation sequencing data

Software Tools for the Genomics Community

As the rate of genomic progress continues to accelerate, so does the need for new tools and knowledge-sharing within the research community. At Illumina, we believe collaboration plays a key role in advancing the possibilities of genomics.

That’s why we develop a variety of bioinformatics tools and share them on Github, an open-source software sharing platform. This way, researchers around the world can continually test, iterate, and share updates with the genomic community.

These open-source bioinformatics tools are free and available on Github. Explore the list below to find tools that meet your specific needs.

Featured Open-Source Bioinformatics Tools


A tool to genotype the drug-metabolizing enzyme gene CYP2D6 using whole-genome sequencing data.


A tool for genotyping repeats and detecting repeat expansions.


A suite of graph-based genotyping tools, specifically optimized for structural variants in short-read sequencing data.


A deep residual neural network for classifying the pathogenicity of missense mutations.


A computational method for visualization of sequencing data in genomic regions containing long repeat expansions.

SMN CopyNumberCaller

A copy number caller for SMN1 and SMN2 to enable spinal muscular atrophy and carrier screening studies using whole-genome sequencing data.


A deep learning-based tool to identify splice variants and predict splice junctions.

Strelka2 Small Variant Caller

A fast, accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.

Genomic Analysis Pipeline Improvements

The Broad Institute and Illumina have partnered to co-develop and improve upon genomic analysis pipelines. Eric Banks of the Broad Institute highlights the development and ehnancement of a DRAGEN-GATK Best Practices pipeline. He also explains how the development team assessed functional equivalency between the open source and licensed version of the pipeline.

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User-Friendly Commercial Bioinformatics Software Tools

DRAGEN Bio-IT Platform

Provides accurate, ultra-rapid secondary genomic analysis of sequencing data for diverse applications.

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BaseSpace Sequence Hub

Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing operations.

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Illumina Connected Analytics

A modular, secure data platform for scalable multiomics data management, analysis, and exploration.

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