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@USDA-ARS-GBRU

USDA-ARS Genomics and Bioinformatics Research Unit

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  1. itsxpress Public

    Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis

    Python 14 11

  2. GuideMaker Public

    GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

    Python 9 3

  3. micrompn Public

    MicroMPN: A Python command line program for automating most probable number (MPN) estimates in microtiter plates

    Python 1 1

  4. PanPipes Public

    Test sets and pipeline scripts for pan-genomic graph analysis

    Python 16 2

  5. branchwater-web Public

    web app for search of SRA with Mastiff

    HTML 2

Repositories

Showing 10 of 76 repositories
  • or_primers Public

    Prototype for using Mixed Integer Linear Programming to optimize multiplex primers

    Python 0 0 0 0 Updated Mar 25, 2025
  • itsxpress Public

    Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis

    Python 14 11 1 0 Updated Mar 20, 2025
  • Spectra Public

    Whole chromosome visualization tool

    Python 0 0 0 0 Updated Mar 20, 2025
  • cep_optimizer Public

    A mixed integer linear programming solution to FNS CEP programs

    Python 0 0 0 0 Updated Mar 12, 2025
  • StandardizedHeterozygosityEvaluation Public
    Shell 0 1 0 0 Updated Mar 10, 2025
  • seed-microbiome-traits Public
    R 0 0 0 0 Updated Mar 10, 2025
  • SugarcaneCrossingTool Public
    R 0 0 4 0 Updated Feb 22, 2025
  • SalmoVar Public

    Salmonella variant-calling pipeline

    0 MIT 0 0 0 Updated Feb 3, 2025
  • PanPipes Public

    Test sets and pipeline scripts for pan-genomic graph analysis

    Python 16 2 0 0 Updated Jan 30, 2025
  • tamipami Public

    A tool for finding the TAM and PAM sites of new Cas and transposon endonucleases from NGS screens

    Python 1 1 1 0 Updated Jan 17, 2025
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