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ascatNgs
Somatic copy number analysis using WGS paired end wholegenome sequencingBRASS
Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.cgpBattenberg
Battenberg algorithm and associated implementation scriptalleleCount
Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele [ACGT] at that location (given any filter settings)dockstore-cgpwgs
Dockstore implementation of CGP core WGS analysiscgpBigWig
BigWig manpulation tools using libBigWig and htslibcgpPindel
Cancer Genome Project Insertion/Deletion detection pipeline based around PindelClusterSV
SV clusteringvafCorrect
Calculates the Variant Allele Fraction of variants in VCF filestelomerecat
Telomerecat: The telomere computational analysis toolNanoSeq
Analysis software for Nanorate Sequencing (NanoSeq) experimentsSimSvGenomes
Simulation of somatically rearranged genomesPCAP-core
NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)VAGrENT
A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequencesdockstore-cgpmap
Mapping using PCAPcgpCaVEManWrapper
Reference implementation of CGP workflow for CaVEMan SNV analysiscgpRna
VaLiAnT
Variant Library Annotation Tool (VaLiAnT) is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experimentsgrass
Gene Rearrangement AnalySiSpyCRISPRcleanR
Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targetingAutoCSA
LEGACY: AutoCSA (Automatic Comparative Sequence Analysis) is a mutation detection program designed to detect small mutations (1-50 bases) in capillary sequence traces. The software is capable of detecting both homozygous and heterozygous base substitutions, as well as small insertions and deletions, to a high sensitivity.dockstore-cgpwxs
Dockstore implementation of CGP core WXS analysiscgpNgsQc
Collection of code for checking NSG sequencing resultscgpbox
DEPRECATED please see dockstore-cgpwgsproportionalmultibw
JBrowse plugin to display multiple BigWig tracks as a stacked proportionstrelka2-manta
Container for strelka2 and mantaRCRISPR
R library for CRISPR analysiscgpCaVEManPostProcessing
Flagging add on to CaVEManppcg-qc-from-sanger
The tools is used to extract PPCG defined QC metrics from Sanger variant calling pipeline results.telomerehunter-docker
Repository to generate docker image for telomerehunterPerlSvAnalysisLib
Object-oriented Perl library for somatic rearrangement analysisWwDocker
(WildWest) Docker - Docker host manager using RabbitMQvcf_flag_modifier
Python application to remove specific flags from VCF filesgripss
Container for the GRIPSS filtering tool ( hartwigmedical / hmftools) for filtering GRIDSS resutlspycroquet
python Crispr Read to Oligo QUantification and Evaluation ToolcgpAnalyseHub
Tools to automate CGHub repository download and process with CGP analysis pipelines.C-SAR
Data will be added ahead of poster/conferencesPlot
Supporting code for Sequence and somatic variation plotsdocker-sigprofiler
cgpJBrowseToolkit
Holds publicly useful scripts and tools for JBrowse users and adminsdockstore-biobambam2
Dockstore implementation of bamtofastq (biobambam2)CASM-Smart-Phase
Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)TraFiC
DEPRECATED please see https://gitlab.com/mobilegenomes/TraFiCpygas
python Guide aligned SequencesBRASS-wdl
WDL descriptor for BRASSQUANTS
cgp-dockstore
Contains scripts and packer builds for cgp-dockstore and Openstack buildskourami-docker
Dockerfile for Kourami assembler for HLA haplotypescrisprReadCountsPy
A tool to count reads for CRISPR.Love Open Source and this site? Check out how you can help us