Repositories list

• ugbio-utils

  Public
  Ultima Genomics bioinfo-utils

  Python

  •1•1•0•11•Updated Aug 21, 2025Aug 21, 2025

• jalign

  Public
  Alignment for SV/CNV calls

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•1•Updated Aug 20, 2025Aug 20, 2025

• parascopy

  Public
  Copy number estimation and variant calling for duplicated genes using WGS.

  Python

  •

  MIT License

  •4•0•0•1•Updated Aug 20, 2025Aug 20, 2025

• gatk

  Public
  Official code repository for GATK versions 4 and up

  Java

  •

  Other

  •610•0•0•4•Updated Aug 12, 2025Aug 12, 2025

• healthomics-workflows

  Public
  UltimaGenomics repository for workflows compatible with AWS HealthOmics

  WDL

  •5•17•2•1•Updated Aug 10, 2025Aug 10, 2025

• hmftools

  Public
  Various algorithms for analysing genomics data

  Java

  •

  GNU General Public License v3.0

  •62•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• gridss

  Public
  GRIDSS: the Genomic Rearrangement IDentification Software Suite

  Java

  •

  Other

  •73•0•0•0•Updated Aug 6, 2025Aug 6, 2025

• VariantCalling

  Public
  Ultima scripts related to downstream processing of WGS, MRD, methylation analysis

  Jupyter Notebook

  •

  Apache License 2.0

  •0•9•5•4•Updated Jul 28, 2025Jul 28, 2025

• HLA-LA

  Public
  Fast HLA type inference from whole-genome data

  C++

  •

  GNU General Public License v3.0

  •42•0•0•0•Updated Jul 17, 2025Jul 17, 2025

• cn.mops

  Public
  Fork of Bioconductor git repository for cn.mops. Contains UG-specific changes

  R

  •4•0•0•1•Updated May 27, 2025May 27, 2025

• picard

  Public
  A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

  Java

  •

  MIT License

  •380•0•0•0•Updated May 25, 2025May 25, 2025

• igv

  Public
  Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

  Java

  •

  MIT License

  •397•0•0•0•Updated May 17, 2025May 17, 2025

• wgbs_tools

  Public
  tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

  Python

  •

  Other

  •46•0•0•0•Updated Dec 24, 2024Dec 24, 2024

• FREEC

  Public
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

  C++

  •51•1•0•0•Updated Aug 26, 2024Aug 26, 2024

• ec2-github-runner

  Public
  On-demand self-hosted AWS EC2 runner for GitHub Actions

  JavaScript

  •

  MIT License

  •369•0•0•0•Updated Aug 11, 2024Aug 11, 2024

• SigProfilerAssignment

  Public
  Assignment of known mutational signatures to individual samples and individual somatic mutations

  Python

  •

  BSD 2-Clause "Simplified" License

  •15•0•0•0•Updated Jun 24, 2024Jun 24, 2024

• STAR

  Public
  RNA-seq aligner

  C

  •

  MIT License

  •530•0•0•0•Updated Feb 15, 2024Feb 15, 2024

• UXM_deconv

  Public
  Python

  •

  Other

  •16•0•0•0•Updated Jan 4, 2023Jan 4, 2023

• leviosam2

  Public
  Fast and accurate coordinate conversion between assemblies

  C++

  •

  MIT License

  •17•0•0•0•Updated Nov 26, 2022Nov 26, 2022

• delly

  Public
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •139•0•0•0•Updated Sep 13, 2022Sep 13, 2022

• test-lfs

  Public
  test git lfs issues

  0•0•0•0•Updated May 17, 2022May 17, 2022

• levioSAM

  Public
  Lift-over alignments from variant-aware references

  C++

  •

  MIT License

  •4•0•0•0•Updated Apr 1, 2022Apr 1, 2022