fqgrep

Grep for FASTQ files.

Search a pair of fastq files for reads that match a given ref or alt sequence.

Install

From bioconda

conda install -c bioconda fqgrep

From Source

git clone ... && cd fqgrep
cargo install --path .

Usage

fqgrep -r 'GACGAGATTA' -a 'GACGTGATTA' --r1-fastq /data/testR1.fastq.gz  --r2-fastq /data/testR2.fastq.gz -o ./test_out -t 28

Help

See the following for usage:

fqgrep -h