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
Cyrius
A tool to genotype the drug-metabolizing enzyme gene CYP2D6 using whole-genome sequencing data.
ExpansionHunter
A tool for genotyping repeats and detecting repeat expansions.
Paragraph
A suite of graph-based genotyping tools, specifically optimized for structural variants in short-read sequencing data.
PrimateAI
A deep residual neural network for classifying the pathogenicity of missense mutations.
REViewer
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.
SpliceAI
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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