CASM IT's repositories
SimSvGenomes
Simulation of somatically rearranged genomes
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
proportionalmultibw
JBrowse plugin to display multiple BigWig tracks as a stacked proportion
PerlSvAnalysisLib
Object-oriented Perl library for somatic rearrangement analysis
cgp-dockstore
Contains scripts and packer builds for cgp-dockstore and Openstack builds
cgpAnalyseHub
Tools to automate CGHub repository download and process with CGP analysis pipelines.
dockstore-biobambam2
Dockstore implementation of bamtofastq (biobambam2)
indelsClassification
R function for the classification of small insertions and deletions for mutational signature analysis
archCompare
Compares pair of archives, files and folders using user configured tools
cgp-methpipe
CGP implementation of Nextflow methylseq
cgpBinCounts
Generates bin count files as required by PICNIC-NGS and some other tools
docker-cgpNgsQC
packec cgpNgsQC
dockstore-cgp-seqval
Dockstore cwl and docker container for validating interleaved fastq files
dockstore-FALCON
Intended for internal use. A CASM Docker image to enable FALCON assembly runs
dockstore-samtools-biobambam2
Docker to provide combinations of samtools and biobambam2
hf-training
Sandbox repository for trying out git-hubflow
RSeQC
fork of RSeQC python RNAseq metrics suit of tools
tophat
Spliced read mapper for RNA-Seq
wr
High performance Workflow Runner