bcl2fq-stats

Illumina sequencing data is always demultiplexed with Bcl2fastq, but it's not always easy to get a table of read counts from the demultiplexed data. bcl2fq-stats is designed to give a quick overview of read count distribution over the given indices, and identify potential index mismatches from the undetermined read counts.

Usage

The program takes Stats.json in the bcl2fastq output folder as input:

bcl2fq-stats --json-file data/Stats.json

Installation

git clone https://github.com/wckdouglas/bcl2fq-stats.git
cd bcl2fq-stats
cargo install --path .

or using docker:

docker pull ghcr.io/wckdouglas/bcl2fq-stats:main