Repositories list

• biotrain-bootcamp-website

  Public
  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…

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 28, 2026May 28, 2026

• STITCH

  Public
  STITCH - Sequencing To Imputation Through Constructing Haplotypes

  C

  •

  GNU General Public License v3.0

  •2424 forks•00 stars•00 issues•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• Hauser_MAPT_MPRAs

  Public
  Scripts associated with Hauser et al. 2026

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 27, 2026Mar 27, 2026

• Burden-Analysis

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 11, 2026Feb 11, 2026

• Run-Tractor

  Public
  A pipeline used to prepare files for Tractor-Mix. Performs phasing with shapeit5 and local ancestry with rfmix2.

  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• vep-configs

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 1, 2025Oct 1, 2025

• talos

  Public
  Fork for HudsonAlpha deployment of populationgenomics/talos

  Python

  •

  MIT License

  •1919 forks•22 stars•00 issues•00 pull requests•Updated Sep 22, 2025Sep 22, 2025

• iTF-Microglia

  Public
  All code generated for Rodriguez-Nunez et al. 2025

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 11, 2025Sep 11, 2025

• ClinvArbitration

  Public
  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

  •33 forks•00 stars•00 issues•00 pull requests•Updated Sep 3, 2025Sep 3, 2025

• Pre-Imputation-QC-Pipeline

  Public
  Shell

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 17, 2025Apr 17, 2025

• CSL_public_benchmark

  Public
  Location of public benchmarking; primarily final results

  Shell

  •

  Apache License 2.0

  •00 forks•1818 stars•00 issues•00 pull requests•Updated Feb 17, 2025Feb 17, 2025

• Generate-PRS

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 30, 2024Oct 30, 2024

• jasmine_sv_annotations

  Public
  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

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 19, 2024Aug 19, 2024

• Check-Concordance

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 6, 2024Aug 6, 2024

• PRS-Pipeline

  Public
  R

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jul 24, 2024Jul 24, 2024

• igv-grapher

  Public
  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

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jul 24, 2024Jul 24, 2024

• STEVE

  Public
  Python

  •

  Apache License 2.0

  •11 fork•1010 stars•00 issues•00 pull requests•Updated Mar 7, 2024Mar 7, 2024

• Post-Imputation-Pipeline

  Public
  Shell

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jul 26, 2023Jul 26, 2023

• rust-fastleng

  Public
  a fastx parser for generating sequence length metrics

  rustgenomicsnext-generation-sequencing+ 4

  rustgenomicsnext-generation-sequencingfastafastqquality-metricslong-read-sequencing

  Rust

  •

  Other

  •00 forks•22 stars•00 issues•00 pull requests•Updated Apr 20, 2023Apr 20, 2023

• fmlrc2

  Public
  rustgenomicsbwt+ 2

  rustgenomicsbwterror-correctionlong-read-sequencing

  Rust

  •

  Apache License 2.0

  •55 forks•4949 stars•00 issues•00 pull requests•Updated Mar 19, 2023Mar 19, 2023

• poison_exon_variant_analysis

  Public
  This repository details the poison exon analysis detailed in Felker et al.

  R

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 8, 2023Mar 8, 2023

• rust-msbwt

  Public
  place for building up a msbwt resource in Rust

  rustgenomicsnext-generation-sequencing+ 2

  rustgenomicsnext-generation-sequencingbwtmsbwt

  Rust

  •

  Apache License 2.0

  •22 forks•1010 stars•22 issues•00 pull requests•Updated Feb 1, 2023Feb 1, 2023

• postgres-operator-examples

  Public
  Examples for deploying applications with PGO, the Postgres Operator from Crunchy Data

  Smarty

  •

  Apache License 2.0

  •6.6k6.6k forks•00 stars•00 issues•00 pull requests•Updated Oct 8, 2021Oct 8, 2021

• k3s-ansible

  Public
  HTML

  •

  Apache License 2.0

  •966966 forks•00 stars•00 issues•00 pull requests•Updated Sep 19, 2021Sep 19, 2021

• mixoviz

  Public
  Detection and visualization of 2n/3n mixoploidy from a VCF

  Python

  •

  Other

  •22 forks•22 stars•00 issues•00 pull requests•Updated May 20, 2021May 20, 2021

• simple_cromwell_example

  Public
  An example WDL workflow, input json, and croo json to demonstrate use of HudsonAlpha's Cromwell CLI

  WDL

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2020Apr 8, 2020

• Python2_3_Conversion

  Public
  Repo for the python conversion work

  00 forks•00 stars•00 issues•00 pull requests•Updated Nov 11, 2019Nov 11, 2019

• VarSight

  Public
  Python

  •

  Other

  •33 forks•1010 stars•00 issues•00 pull requests•Updated Oct 21, 2019Oct 21, 2019

• UDN_SV_export

  Public
  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated May 21, 2019May 21, 2019

• LayeredGraph

  Public
  Methods for building layered graphs and running graph traversal algorithms

  Python

  •

  Other

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 19, 2019Jan 19, 2019