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Illumina

Illumina Open Source Software

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  1. SpliceAI SpliceAI Public

    A deep learning-based tool to identify splice variants

    Python 465 174

  2. hap.py hap.py Public

    Haplotype VCF comparison tools

    C++ 448 130

  3. manta manta Public archive

    Structural variant and indel caller for mapped sequencing data

    C++ 447 154

  4. strelka strelka Public

    Strelka2 germline and somatic small variant caller

    C++ 386 108

  5. ExpansionHunter ExpansionHunter Public

    A tool for estimating repeat sizes

    C++ 198 57

  6. Nirvana Nirvana Public

    The nimble & robust variant annotator

    C# 186 49

Repositories

Showing 10 of 56 repositories
  • PrimateAI-3D Public
    Illumina/PrimateAI-3D’s past year of commit activity
    Python 72 12 6 0 Updated Oct 26, 2025
  • IlluminaConnectedAnnotationsDocumentation Public
    Illumina/IlluminaConnectedAnnotationsDocumentation’s past year of commit activity
    MDX 1 1 0 0 Updated Oct 23, 2025
  • GTCtoVCF Public

    Script to convert GTC/BPM files to VCF

    Illumina/GTCtoVCF’s past year of commit activity
    Python 47 Apache-2.0 30 16 1 Updated Oct 13, 2025
  • manta Public archive

    Structural variant and indel caller for mapped sequencing data

    Illumina/manta’s past year of commit activity
    C++ 447 154 128 2 Updated Oct 11, 2025
  • dragen-aws-batch-quickstart Public
    Illumina/dragen-aws-batch-quickstart’s past year of commit activity
    HTML 7 Apache-2.0 5 0 0 Updated Jul 30, 2025
  • SpliceAI Public

    A deep learning-based tool to identify splice variants

    Illumina/SpliceAI’s past year of commit activity
    Python 465 174 28 4 Updated Jul 18, 2025
  • PromoterAI Public
    Illumina/PromoterAI’s past year of commit activity
    Python 80 13 2 0 Updated Jun 22, 2025
  • interop Public

    C++ Library to parse Illumina InterOp files

    Illumina/interop’s past year of commit activity
    C++ 79 GPL-3.0 28 4 0 Updated Jun 14, 2025
  • BeadArrayFiles Public

    Python library to parse file formats related to Illumina bead arrays

    Illumina/BeadArrayFiles’s past year of commit activity
    Python 48 35 15 2 Updated Jan 30, 2025
  • Bench-Example-Images Public
    Illumina/Bench-Example-Images’s past year of commit activity
    Shell 4 0 0 0 Updated Sep 27, 2024
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