cancerit/CaVEMan

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C
License
GNU Affero Genera...
Created over 10 years ago
Updated 5 months ago

cancerit/CaVEMan

cancerit

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SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib

ascatNgs

Somatic copy number analysis using WGS paired end wholegenome sequencing

BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.

cgpBattenberg

Battenberg algorithm and associated implementation script

alleleCount

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 analysis

cgpBigWig

BigWig manpulation tools using libBigWig and htslib

cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

ClusterSV

vafCorrect

Calculates the Variant Allele Fraction of variants in VCF files

telomerecat

Telomerecat: The telomere computational analysis tool

NanoSeq

Analysis software for Nanorate Sequencing (NanoSeq) experiments

SimSvGenomes

Simulation of somatically rearranged genomes

PCAP-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 consequences

dockstore-cgpmap

Mapping using PCAP

Common Workflow Language

cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis

cgpRna

VaLiAnT

Variant Library Annotation Tool (VaLiAnT) is an oligonucleotide library design and annotation tool for Saturation Genome Editing and other Deep Mutational Scanning experiments

grass

Gene Rearrangement AnalySiS

pyCRISPRcleanR

Python version of CRISPRcleanR: An R package for unsupervised identification and correction of gene independent cell responses to CRISPR-cas9 targeting

AutoCSA

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 analysis

cgpNgsQc

Collection of code for checking NSG sequencing results

cgpbox

DEPRECATED please see dockstore-cgpwgs

proportionalmultibw

JBrowse plugin to display multiple BigWig tracks as a stacked proportion

strelka2-manta

Container for strelka2 and manta

RCRISPR

R library for CRISPR analysis

cgpCaVEManPostProcessing

Flagging add on to CaVEMan

ppcg-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 telomerehunter

PerlSvAnalysisLib

Object-oriented Perl library for somatic rearrangement analysis

WwDocker

(WildWest) Docker - Docker host manager using RabbitMQ

vcf_flag_modifier

Python application to remove specific flags from VCF files

gripss

Container for the GRIPSS filtering tool ( hartwigmedical / hmftools) for filtering GRIDSS resutls

pycroquet

python Crispr Read to Oligo QUantification and Evaluation Tool

Jupyter Notebook

cgpAnalyseHub

Tools to automate CGHub repository download and process with CGP analysis pipelines.

C-SAR

Data will be added ahead of poster/conference

sPlot

Supporting code for Sequence and somatic variation plots

docker-sigprofiler

cgpJBrowseToolkit

Holds publicly useful scripts and tools for JBrowse users and admins

dockstore-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/TraFiC

pygas

python Guide aligned Sequences

BRASS-wdl

WDL descriptor for BRASS

QUANTS

cgp-dockstore

Contains scripts and packer builds for cgp-dockstore and Openstack builds

kourami-docker

Dockerfile for Kourami assembler for HLA haplotypes

crisprReadCountsPy

A tool to count reads for CRISPR.