DISCVR-seq Toolkit is a diverse collection of tools for working with sequencing data, developed and maintained by the Bimber Lab, built using the GATK4 engine. The set of tools is analogous to GATK or Picard. A description of all software produced by the Bimber Lab can be found here.
Please view our documentation for more information about the set of tools and usage.
While DISCVR-seq contains many useful tools that will not be published, a handful of the tools have their own publications:
| Tool | Description | Citation |
|---|---|---|
| VariantQC | Creates an HTML report summarizing VCF data | VariantQC: a visual quality control report for variant evaluation. Yan MY, Ferguson B, Bimber BN. Bioinformatics. 2019 Dec 15;35(24):5370-5371. PMID: 31309221 |
| IntegrationSiteMapper | Detect and summarize transgene integration | Ryu et. al, Under Review |
DISCVR-seq Toolkit is a java program distributed as a single JAR. You can download the latest JAR from our release page. Running tools is analogous to GATK4.
While we recommend our documentation to learn about available tools and options, one can also list arguments from the command line:
# View arguments for a specific tool (VariantQC in this example):
java -jar DISCVRseq.jar VariantQC --help
By popular demand, DISCVR-seq releases are available as docker images, via GitHub Packages. We recommend using a specific release, which you can do using tags:
# Pull specific version:
docker pull ghcr.io/bimberlab/discvrseq:1.20
# Pull latest version:
docker pull ghcr.io/bimberlab/discvrseq:latest
# Or:
docker pull ghcr.io/bimberlab/discvrseq
# Running the container will automatically run DISCVRseq (equivalent to java -jar DISCVRseq.jar ...):
docker run ghcr.io/bimberlab/discvrseq VariantQC --help