DKFZ - ODCF
GitHub organization for the DKFZ Omics IT and Data Management Core Facility
DKFZ, Heidelberg, Germany
Pinned Repositories
ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
AlignmentAndQCWorkflows
The DKFZ alignment workflow plugin originally developed at the eilslabs
DKFZBiasFilter
IndelCallingWorkflow
A Platypus-based workflow for indel calling
ldap-summary
Simple shellscripts to make interaction with LDAP/AD/ldapsearch easier
methylCtools-fingerprint
Fingerprinting code originally part of the the methylCtools of Volker Hovestadt.
nf-bam2fastq
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
RNAseqWorkflow
Roddy RNA-seq Workflow Plugin
SNVCallingWorkflow
The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow
SophiaWorkflow
A Roddy plugin to run the Sophia tool.
DKFZ - ODCF's Repositories
DKFZ-ODCF/ACEseqWorkflow
Allele-specific copy number estimation with whole genome sequencing
DKFZ-ODCF/DKFZBiasFilter
DKFZ-ODCF/SNVCallingWorkflow
The DKFZ-ODCF, formerly DKFZ/eilslabs SNV-Calling Workflow
DKFZ-ODCF/AlignmentAndQCWorkflows
The DKFZ alignment workflow plugin originally developed at the eilslabs
DKFZ-ODCF/RNAseqWorkflow
Roddy RNA-seq Workflow Plugin
DKFZ-ODCF/IndelCallingWorkflow
A Platypus-based workflow for indel calling
DKFZ-ODCF/ldap-summary
Simple shellscripts to make interaction with LDAP/AD/ldapsearch easier
DKFZ-ODCF/SophiaWorkflow
A Roddy plugin to run the Sophia tool.
DKFZ-ODCF/methylCtools-fingerprint
Fingerprinting code originally part of the the methylCtools of Volker Hovestadt.
DKFZ-ODCF/nf-bam2fastq
Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.
DKFZ-ODCF/sophia
The Sophia structural variation caller. Fork of https://bitbucket.org/utoprak/sophia.
DKFZ-ODCF/COWorkflowsBasePlugin
A basic Roddy plugin for computational oncology workflows
DKFZ-ODCF/ega-cluster-cryptor
parallelise encryption of EGA submissions onto a cluster - a partial EgaCryptor replacement
DKFZ-ODCF/FastqIndEx
A tool to index and extract data from gzipped FASTQ files
DKFZ-ODCF/ega-xml-dl
batch download everything in your EGA or ENA submission account
DKFZ-ODCF/example-cwlexec-singularity
An example CWL workflow to be run with Singularity on an LSF cluster
DKFZ-ODCF/igv-crawler
Crawl any filesystem for genome data, providing one-click opening in IGV. READ ONLY REPOSITORY.
DKFZ-ODCF/odcf-guide
Read-Only mirror; please see GitLab for main repo
DKFZ-ODCF/bioinformatic-reproducibility-course
A course on basic tools for reproducibility in bioinformatics
DKFZ-ODCF/nf-arriba
DKFZ-ODCF/reference-data
Code to setup and maintain reference assemblies and accompanying data
DKFZ-ODCF/COWorkflows
Legacy repository for the COWorkflows plugin
DKFZ-ODCF/FastqIndEx-integration-testing
Test script(s) to perform integration tests for the FastqIndEx'er
DKFZ-ODCF/methylCtools
analysis of whole-genome bisulfite sequencing data
DKFZ-ODCF/setup-reference-data
Code and documentation for setting up reference data for the DKFZ-ODCF workflows, including reference genomes and their supplementary files, annotation data, etc.
DKFZ-ODCF/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see