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.
View WebinarUser-Friendly Commercial Bioinformatics Software Tools
DRAGEN secondary analysis
Provides accurate, ultra-rapid secondary genomic analysis of sequencing data for diverse applications.
View SoftwareBaseSpace Sequence Hub
Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing operations.
View SoftwareIllumina Connected Analytics
A modular, secure data platform for scalable multiomics data management, analysis, and exploration.
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Bioinformatics Pipeline Setup
We offer a variety of resources and information to help simplify the process of setting up your informatics infrastructure and data analysis pipeline.
Sequencing Data Analysis
Our sequencing data analysis software helps you spend more time doing research, and less time configuring and running analysis workflows.
DRAGEN Publications
See a list of publications summarizing the extensive applications of DRAGEN secondary analysis.