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    • STITCH

      Public
      STITCH - Sequencing To Imputation Through Constructing Haplotypes
      C
      GNU General Public License v3.0
      23000Updated Apr 9, 2026Apr 9, 2026
    • Scripts associated with Hauser et al. 2026
      Jupyter Notebook
      0000Updated Mar 27, 2026Mar 27, 2026
    • Shell
      0000Updated Feb 11, 2026Feb 11, 2026
    • A pipeline used to prepare files for Tractor-Mix. Performs phasing with shapeit5 and local ancestry with rfmix2.
      Shell
      0000Updated Feb 5, 2026Feb 5, 2026
    • This repository was previously hosted at james-lawlor.github.io and was the biotrain bootcamp website where we posted slides and an overview of the computationa…
      0000Updated Jan 26, 2026Jan 26, 2026
    • Shell
      0000Updated Oct 1, 2025Oct 1, 2025
    • talos

      Public
      Fork for HudsonAlpha deployment of populationgenomics/talos
      Python
      MIT License
      13200Updated Sep 22, 2025Sep 22, 2025
    • All code generated for Rodriguez-Nunez et al. 2025
      R
      MIT License
      0000Updated Sep 11, 2025Sep 11, 2025
    • A side-project from the AIP, containing the code, logic, and documentation for the ClinVar consequence reassessment process in use at the CPG
      Python
      MIT License
      3000Updated Sep 3, 2025Sep 3, 2025
    • Shell
      1000Updated Apr 17, 2025Apr 17, 2025
    • Location of public benchmarking; primarily final results
      Shell
      Apache License 2.0
      01800Updated Feb 17, 2025Feb 17, 2025
    • Shell
      0000Updated Oct 30, 2024Oct 30, 2024
    • A pipeline to merge 2 or more sample SV VCFs into a consensus set and annotate with frequency resources with merging via jasmine
      Python
      MIT License
      0100Updated Aug 19, 2024Aug 19, 2024
    • Shell
      0000Updated Aug 6, 2024Aug 6, 2024
    • R
      1000Updated Jul 24, 2024Jul 24, 2024
    • Given a BED file and either a bed file of genomic regions or VCF of structural variant calls, use IGV in headless mode to make graphs.
      Python
      MIT License
      0200Updated Jul 24, 2024Jul 24, 2024
    • STEVE

      Public
      Python
      Apache License 2.0
      11000Updated Mar 7, 2024Mar 7, 2024
    • Shell
      0000Updated Jul 26, 2023Jul 26, 2023
    • a fastx parser for generating sequence length metrics
      Rust
      Other
      0200Updated Apr 20, 2023Apr 20, 2023
    • fmlrc2

      Public
      Rust
      Apache License 2.0
      54900Updated Mar 19, 2023Mar 19, 2023
    • This repository details the poison exon analysis detailed in Felker et al.
      R
      MIT License
      0100Updated Mar 8, 2023Mar 8, 2023
    • place for building up a msbwt resource in Rust
      Rust
      Apache License 2.0
      21020Updated Feb 1, 2023Feb 1, 2023
    • Examples for deploying applications with PGO, the Postgres Operator from Crunchy Data
      Smarty
      Apache License 2.0
      6.5k000Updated Oct 8, 2021Oct 8, 2021
    • HTML
      Apache License 2.0
      957000Updated Sep 19, 2021Sep 19, 2021
    • mixoviz

      Public
      Detection and visualization of 2n/3n mixoploidy from a VCF
      Python
      Other
      2200Updated May 20, 2021May 20, 2021
    • An example WDL workflow, input json, and croo json to demonstrate use of HudsonAlpha's Cromwell CLI
      WDL
      0000Updated Apr 8, 2020Apr 8, 2020
    • Repo for the python conversion work
      0000Updated Nov 11, 2019Nov 11, 2019
    • VarSight

      Public
      Python
      Other
      31000Updated Oct 21, 2019Oct 21, 2019
    • MIT License
      1100Updated May 21, 2019May 21, 2019
    • Methods for building layered graphs and running graph traversal algorithms
      Python
      Other
      2000Updated Jan 19, 2019Jan 19, 2019
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