Awesome
fqgrep
<p align="center"> <a href="https://github.com/fulcrumgenomics/fqgrep/actions?query=workflow%3ACheck"><img src="https://github.com/fulcrumgenomics/fqgrep/workflows/Check/badge.svg" alt="Build Status"></a> <img src="https://img.shields.io/crates/l/fqgrep.svg" alt="license"> <a href="https://crates.io/crates/fqgrep"><img src="https://img.shields.io/crates/v/fqgrep.svg?colorB=319e8c" alt="Version info"></a> <a href="http://bioconda.github.io/recipes/fqgrep/README.html"><img src="https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat" alt="Install with bioconda"></a> <br> Grep for FASTQ files. </p>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