Repositories list

• pipeline5

  Public
  Java

  •

  GNU General Public License v3.0

  •3•19•0•3•Updated Dec 25, 2024Dec 25, 2024

• hmftools

  Public
  Various algorithms for analysing genomics data

  Java

  •

  GNU General Public License v3.0

  •60•200•7•5•Updated Dec 24, 2024Dec 24, 2024

• scripts

  Public
  Shell

  •

  GNU General Public License v3.0

  •14•20•2•8•Updated Dec 23, 2024Dec 23, 2024

• serve

  Public
  SERVE and dependencies

  Java

  •

  GNU General Public License v3.0

  •0•0•0•1•Updated Dec 19, 2024Dec 19, 2024

• platinum

  Public
  Run multiple Pipeline5 instances at once

  Java

  •

  GNU General Public License v3.0

  •1•10•2•0•Updated Dec 18, 2024Dec 18, 2024

• cram2fastq

  Public
  Convert CRAM files stored in GCP to FASTQ

  Shell

  •0•1•0•0•Updated Oct 11, 2024Oct 11, 2024

• bamcomp

  Public
  Tools for comparing BAMs and CRAMs

  Java

  •0•1•0•2•Updated Oct 3, 2024Oct 3, 2024

• actin-interview

  Public
  ACTIN development interview case

  Kotlin

  •0•0•0•0•Updated Jul 4, 2024Jul 4, 2024

• snpcheck

  Public
  A post-pipeline validation which compares the results of the unifiedgenotyper against a control VCF as a final QC

  Java

  •0•0•0•0•Updated May 8, 2024May 8, 2024

• peach

  Public
  Describe PEACH

  Python

  •0•1•0•0•Updated Jan 5, 2024Jan 5, 2024

• documentation

  Public
  Welcome to Hartwig Medical Foundation’s documentation site!

  HTML

  •3•1•0•0•Updated Oct 26, 2023Oct 26, 2023

• k8analysis

  Public
  Run data analysis jobs in Kubernetes

  Python

  •0•1•0•0•Updated Apr 25, 2023Apr 25, 2023

• gridss

  Public
  GRIDSS: the Genomic Rearrangement IDentification Software Suite

  Java

  •

  Other

  •71•0•0•0•Updated Mar 18, 2023Mar 18, 2023

• hartwigmedical.github.io

  Public archive
  HTML

  •0•0•0•0•Updated Mar 16, 2023Mar 16, 2023

• rna-experiments

  Public
  Repo for various RNA experiments

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 1, 2022Aug 1, 2022

• golden-datasets

  Public
  Download, extract and format golden datasets to benchmark pipelines

  R

  •

  GNU General Public License v3.0

  •3•0•0•0•Updated Jan 21, 2022Jan 21, 2022

• tar-flowcell-bcl

  Public
  Tar flowcell BCL's that are stored at GCP

  Shell

  •0•0•0•0•Updated Sep 23, 2021Sep 23, 2021

• k8-flagstat

  Public archive
  Run sambamba flagstat in kubernetes

  Shell

  •0•0•0•0•Updated Aug 17, 2021Aug 17, 2021

• k8-align

  Public archive
  Align FASTQ and dedup bams in kubernetes

  Shell

  •0•0•0•0•Updated Aug 17, 2021Aug 17, 2021

• testdata

  Public
  Small datasets for testing purpose (FASTQ, BAM)

  GNU General Public License v3.0

  •4•20•0•0•Updated Jul 7, 2021Jul 7, 2021

• dcc-portal

  Public
  Data portal for exploring and accessing data

  JavaScript

  •

  Other

  •8•0•0•0•Updated Mar 24, 2021Mar 24, 2021

• gcpworkshop

  Public
  README to follow along with the GCP workshop from HMF

  1•1•0•0•Updated May 18, 2020May 18, 2020

• frontend-download

  Public archive
  Front end application for use with Schuberg Philis connect portal that enables downloading of genomic data from S3 compatible storage

  JavaScript

  •3•1•0•0•Updated Apr 27, 2020Apr 27, 2020

• pipeline-perl

  Public archive
  Pipeline of tools to process raw fastq data and produce meaningful genomic data

  Perl

  •

  MIT License

  •4•14•0•0•Updated Feb 20, 2020Feb 20, 2020

• dcc-id

  Public
  ID system for ICGC projects

  Java

  •

  Other

  •5•0•0•0•Updated May 14, 2019May 14, 2019

• qc-checks

  Public archive
  Quality Check scripts [OBSOLETE]

  Shell

  •0•0•0•0•Updated Sep 12, 2018Sep 12, 2018

• dcc-release

  Public
  Second generation of the ICGC DCC release ETL built on Spark

  Java

  •

  Other

  •9•0•0•0•Updated Mar 5, 2018Mar 5, 2018

• dcc-import

  Public
  Reference data importers

  Java

  •

  Other

  •4•0•0•0•Updated Mar 2, 2018Mar 2, 2018

• health-checks

  Public archive
  Repo for the HMF health checker [OBSOLETE]

  Java

  •

  MIT License

  •1•1•0•0•Updated Jan 24, 2017Jan 24, 2017