Overview

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.

Published Tools

While DISCVR-seq contains many useful tools that will not be published, a handful of the tools have their own publications: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 J, Chan W, Wettengel JM, Hanna CB, Burwitz BJ, Hennebold JD, Bimber BN. Rapid, accurate mapping of transgene integration in viable rhesus macaque embryos using enhanced-specificity tagmentation-assisted PCR. Mol Ther Methods Clin Dev. 2022 Jan 19;24:241-254. PMID: 35211637.

Getting Started

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

Please note that any tool that uses a reference genome requires this genome to be indexed with samtools and to have a sequence dictionary created with Picard. These requirements are identical to most tools from GATK or Picard. See here for more information

List of Tools

Our complete list of tools and arguments is available here. View each tool’s page for more information about usage.

Docker

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