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actin-interview

ACTIN development interview case

bamcomp

Tools for comparing BAMs and CRAMs

cram2fastq

Convert CRAM files stored in GCP to FASTQ

dcc-id

ID system for ICGC projects

dcc-import

Reference data importers

dcc-portal

Data portal for exploring and accessing data

dcc-release

Second generation of the ICGC DCC release ETL built on Spark

documentation

Welcome to Hartwig Medical Foundation’s documentation site!

frontend-download

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

gcpworkshop

README to follow along with the GCP workshop from HMF

golden-datasets

Download, extract and format golden datasets to benchmark pipelines

gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite

hartwigmedical.github.io

health-checks

Repo for the HMF health checker [OBSOLETE]

hmftools

Various algorithms for analysing genomics data

k8-align

Align FASTQ and dedup bams in kubernetes

k8-flagstat

Run sambamba flagstat in kubernetes

k8analysis

Run data analysis jobs in Kubernetes

oncoact

Algo's used in the OncoAct pipeline

peach

Describe PEACH

pipeline-perl

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

pipeline5

platinum

Run multiple Pipeline5 instances at once

qc-checks

Quality Check scripts [OBSOLETE]

rna-experiments

Repo for various RNA experiments

scripts

serve

SERVE and dependencies

snpcheck

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

tar-flowcell-bcl

Tar flowcell BCL's that are stored at GCP

testdata

Small datasets for testing purpose (FASTQ, BAM)