read-qc-tools

Docker image containing tools for read QC and processing.

Included Tools

• fastqc - Quality control for high throughput sequence data
• multiqc - Aggregate results from bioinformatics analyses
• samtools - Tools for manipulating SAM/BAM files
• python 3.12 with biopython and pysam
• GNU parallel - Shell tool for executing jobs in parallel
• jq - Command-line JSON processor
• pigz - Parallel gzip
• zstd - Zstandard compression

Usage

Pull from GitHub Container Registry

docker pull ghcr.io/broadinstitute/read-qc-tools:main

Run interactively

docker run --rm -it -v $(pwd):/data ghcr.io/broadinstitute/read-qc-tools:main bash

Run a specific command

docker run --rm -v $(pwd):/data ghcr.io/broadinstitute/read-qc-tools:main fastqc reads.fastq.gz

Building Locally

./scripts/build.sh

Or with custom image name/tag:

IMAGE_NAME=my-image TAG=dev ./scripts/build.sh

Multi-Architecture Support

The image is built for both linux/amd64 (Intel/AMD) and linux/arm64 (Apple Silicon, ARM servers). Docker will automatically pull the correct architecture for your platform.

Modifying the Environment

Edit env.yaml to add or remove conda packages, then rebuild.