CASM IT

CaVEMan

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

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)

cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

NanoSeq

Analysis software for Nanorate Sequencing (NanoSeq) experiments

PCAP-core

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

cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis

VaLiAnT

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

pyCRISPRcleanR

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

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.

RCRISPR

R library for CRISPR analysis

telomerehunter-docker

Repository to generate docker image for telomerehunter

C-SAR

Data will be added ahead of poster/conference

CASM-Smart-Phase

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

cgpJBrowseToolkit

Holds publicly useful scripts and tools for JBrowse users and admins

kourami-docker

Dockerfile for Kourami assembler for HLA haplotypes

annotateVCF

Annotate vcf file using user supplied data

cgp-convert-counts

tools for converting RNAseq count data

cgp_seq_input_val

Sequence data and manifest validation code.

cgpBpipe

local repo of bpipe that handles LSF array jobs

cgpVcf

Vcf file utilities

CMScallerWrapper

This is docker image to run CMScaller from

dockstore-pyCRISPRcleanR

Dockersised pyCRISPRcleanR

ExpansionHunter-docker

Dockerfile for ExpansionHunter

hairpin-wrapper

Ease-of-use wrapper around Mathijs' Sanders AdditionalBamStatistics cruciform-DNA detection algorithm

jbrowse-registry

JBrowse Plugin Registry

pyQUEST

QUANTS

ta_analyser

script to analyse ta repeats coverage calculated using samtools bedcov

vcfilter