CASM IT

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)

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.

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

cgpBattenberg

Battenberg algorithm and associated implementation script

cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis

cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

dockstore-cgpwgs

Dockstore implementation of CGP core WGS analysis

proportionalmultibw

JBrowse plugin to display multiple BigWig tracks as a stacked proportion

VAGrENT

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

cancerit/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

cancerit/BRASS

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

cancerit/cgpBigWig

BigWig manpulation tools using libBigWig and htslib

cancerit/cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

cancerit/NanoSeq

Analysis software for Nanorate Sequencing (NanoSeq) experiments

cancerit/PCAP-core

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

cancerit/cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis

cancerit/dockstore-cgpmap

Mapping using PCAP

cancerit/cgpRna

cancerit/VaLiAnT

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

cancerit/pyCRISPRcleanR

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

cancerit/pycroquet

python Crispr Read to Oligo QUantification and Evaluation Tool

cancerit/C-SAR

Data will be added ahead of poster/conference

cancerit/CASM-Smart-Phase

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

cancerit/cgpJBrowseToolkit

Holds publicly useful scripts and tools for JBrowse users and admins

cancerit/crisprReadCountsPy

A tool to count reads for CRISPR.

cancerit/pygas

python Guide aligned Sequences

cancerit/QUANTS

cancerit/vcf_flag_modifier

Python application to remove specific flags from VCF files

cancerit/dockstore-pyCRISPRcleanR

Dockersised pyCRISPRcleanR

cancerit/pyQUEST

cancerit/annotateVCF

Annotate vcf file using user supplied data

cancerit/cgp-methpipe

CGP implementation of Nextflow methylseq

cancerit/cgp_seq_input_val

Sequence data and manifest validation code.

cancerit/CMScallerWrapper

This is docker image to run CMScaller from

cancerit/hairpin2

artefact flagging algorithm based on Ellis et al. 2020 (DOI: 10.1038/s41596-020-00437-6) for LCM sequencing

cancerit/jbrowse-registry

JBrowse Plugin Registry

cancerit/lowinputtrees

cancerit/ta_analyser

script to analyse ta repeats coverage calculated using samtools bedcov

cancerit/vcfilter