Pinned Repositories
bamcomp
Tools for comparing BAMs and CRAMs
health-checks
Repo for the HMF health checker [OBSOLETE]
hmftools
Various algorithms for analysing genomics data
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
scripts
testdata
Small datasets for testing purpose (FASTQ, BAM)
Hartwig Medical Foundation's Repositories
hartwigmedical/hmftools
Various algorithms for analysing genomics data
hartwigmedical/scripts
hartwigmedical/testdata
Small datasets for testing purpose (FASTQ, BAM)
hartwigmedical/pipeline5
hartwigmedical/pipeline-perl
Pipeline of tools to process raw fastq data and produce meaningful genomic data
hartwigmedical/platinum
Run multiple Pipeline5 instances at once
hartwigmedical/bamcomp
Tools for comparing BAMs and CRAMs
hartwigmedical/cram2fastq
Convert CRAM files stored in GCP to FASTQ
hartwigmedical/documentation
Welcome to Hartwig Medical Foundation’s documentation site!
hartwigmedical/frontend-download
Front end application for use with Schuberg Philis connect portal that enables downloading of genomic data from S3 compatible storage
hartwigmedical/gcpworkshop
README to follow along with the GCP workshop from HMF
hartwigmedical/health-checks
Repo for the HMF health checker [OBSOLETE]
hartwigmedical/k8analysis
Run data analysis jobs in Kubernetes
hartwigmedical/oncoact
Algo's used in the OncoAct pipeline
hartwigmedical/peach
Describe PEACH
hartwigmedical/k8-align
Align FASTQ and dedup bams in kubernetes
hartwigmedical/k8-flagstat
Run sambamba flagstat in kubernetes
hartwigmedical/actin-interview
ACTIN development interview case
hartwigmedical/dcc-id
ID system for ICGC projects
hartwigmedical/dcc-import
Reference data importers
hartwigmedical/dcc-portal
Data portal for exploring and accessing data
hartwigmedical/dcc-release
Second generation of the ICGC DCC release ETL built on Spark
hartwigmedical/golden-datasets
Download, extract and format golden datasets to benchmark pipelines
hartwigmedical/gridss
GRIDSS: the Genomic Rearrangement IDentification Software Suite
hartwigmedical/hartwigmedical.github.io
hartwigmedical/qc-checks
Quality Check scripts [OBSOLETE]
hartwigmedical/rna-experiments
Repo for various RNA experiments
hartwigmedical/serve
SERVE and dependencies
hartwigmedical/snpcheck
A post-pipeline validation which compares the results of the unifiedgenotyper against a control VCF as a final QC
hartwigmedical/tar-flowcell-bcl
Tar flowcell BCL's that are stored at GCP