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Illumina Open Source Software

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  1. SpliceAI SpliceAI Public archive

    A deep learning-based tool to identify splice variants

    Python 507 178

  2. hap.py hap.py Public

    Haplotype VCF comparison tools

    C++ 472 135

  3. manta manta Public archive

    Structural variant and indel caller for mapped sequencing data

    C++ 467 157

  4. strelka strelka Public archive

    Strelka2 germline and somatic small variant caller

    C++ 393 106

  5. ExpansionHunter ExpansionHunter Public

    A tool for estimating repeat sizes

    C++ 218 70

  6. Nirvana Nirvana Public archive

    The nimble & robust variant annotator

    C# 196 47

Repositories

Showing 10 of 53 repositories
  • dragen-aws-batch-quickstart Public
    Illumina/dragen-aws-batch-quickstart's past year of commit activity
    HTML 8 Apache-2.0 7 0 1 Updated Apr 22, 2026
  • PrimateAI Public archive

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

    Illumina/PrimateAI's past year of commit activity
    Python 118 32 6 0 Updated Apr 20, 2026
  • interop Public

    C++ Library to parse Illumina InterOp files

    Illumina/interop's past year of commit activity
    C++ 85 29 5 0 Updated Apr 20, 2026
  • Nirvana Public archive

    The nimble & robust variant annotator

    Illumina/Nirvana's past year of commit activity
    C# 196 47 39 5 Updated Apr 20, 2026
  • REViewer Public archive

    A tool for visualizing alignments of reads in regions containing tandem repeats

    Illumina/REViewer's past year of commit activity
    C++ 92 18 35 0 Updated Apr 20, 2026
  • akt Public archive

    Ancestry and Kinship Tools

    Illumina/akt's past year of commit activity
    C++ 70 14 7 2 Updated Apr 20, 2026
  • BlockCompression Public archive

    Block compression library used by Nirvana

    Illumina/BlockCompression's past year of commit activity
    C++ 3 1 0 0 Updated Apr 20, 2026
  • Pisces Public archive

    Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.

    Illumina/Pisces's past year of commit activity
    C# 98 16 55 2 Updated Apr 20, 2026
  • NeoMutalyzer Public archive

    Inspired by Mutalyzer and frustrated by RefSeq, we created this transcript annotation validator

    Illumina/NeoMutalyzer's past year of commit activity
    C# 4 0 0 0 Updated Apr 20, 2026
  • Isaac4 Public archive

    Isaac aligner version 4

    Illumina/Isaac4's past year of commit activity
    C++ 18 3 7 0 Updated Apr 20, 2026
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