We are excited to announce that we will be contributing Illumina’s secondary analysis software to the open source community under the GPL v3 license. The software can be found on GitHub (https://github.com/illumina). Currently available software include the Isaac aligner and the Manta structural variant caller (manuscript submitted). Other tools such as the Starling small variant caller, Strelka somatic variant caller, the Canvas copy number caller, and Haplotype Compare (a.k.a hap.py) for comparing variant call sets will be made available soon. Additional tools will also be made available as they are developed and deployed. With these efforts we are also committing to publication of our methods in high impact peer reviewed journals.
We look forward to working with the open source community to provide high quality secondary analysis tools that will help enable discoveries with next generation sequencing data.