Discover cancerit/NanoSeq Open Source project by CASM IT (@cancerit)

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

CaVEMan

BRASS

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

Battenberg algorithm and associated implementation script

cgpBattenberg

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)

alleleCount

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

BigWig manpulation tools using libBigWig and htslib

cgpBigWig

cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

Calculates the Variant Allele Fraction of variants in VCF files

ClusterSV

SV clustering

vafCorrect

Telomerecat: The telomere computational analysis tool

telomerecat

Simulation of somatically rearranged genomes

SimSvGenomes

PCAP-core

NGS reference implementations and helper code for mapping (originally part of ICGC-TCGA-PanCancer)

A toolset for comparing genomic variants to reference genome annotation to identify potential biological consequences

VAGrENT

Reference implementation of CGP workflow for CaVEMan SNV analysis

dockstore-cgpmap

Mapping using PCAP

Common Workflow Language

cgpCaVEManWrapper

cgpRna

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

VaLiAnT

Gene Rearrangement AnalySiS

grass

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

pyCRISPRcleanR

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.

AutoCSA

Java

dockstore-cgpwxs

Dockstore implementation of CGP core WXS analysis

Collection of code for checking NSG sequencing results

cgpNgsQc

DEPRECATED please see dockstore-cgpwgs

cgpbox

JavaScript

proportionalmultibw

JBrowse plugin to display multiple BigWig tracks as a stacked proportion

JavaScript

strelka2-manta

Container for strelka2 and manta

Dockerfile

RCRISPR

R library for CRISPR analysis

cgpCaVEManPostProcessing

Flagging add on to CaVEMan

The tools is used to extract PPCG defined QC metrics from Sanger variant calling pipeline results.

ppcg-qc-from-sanger

Repository to generate docker image for telomerehunter

telomerehunter-docker

Dockerfile

PerlSvAnalysisLib

Object-oriented Perl library for somatic rearrangement analysis

(WildWest) Docker - Docker host manager using RabbitMQ

WwDocker

Java

vcf_flag_modifier

Python application to remove specific flags from VCF files

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

gripss

Dockerfile

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.

Data will be added ahead of poster/conference

C-SAR

Nextflow

sPlot

Supporting code for Sequence and somatic variation plots

docker-sigprofiler

Holds publicly useful scripts and tools for JBrowse users and admins

cgpJBrowseToolkit

JavaScript

dockstore-biobambam2

Dockstore implementation of bamtofastq (biobambam2)

Docker and associated CASM utility scripts for Smart-Phase (https://github.com/paulhager/smart-phase)

CASM-Smart-Phase

DEPRECATED please see https://gitlab.com/mobilegenomes/TraFiC

TraFiC

python Guide aligned Sequences

pygas

BRASS-wdl

WDL descriptor for BRASS

WDL

QUANTS

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

cgp-dockstore

Dockerfile for Kourami assembler for HLA haplotypes

kourami-docker

A tool to count reads for CRISPR.

crisprReadCountsPy