grepq v1.1.6 is more than 1000 times faster than the venerable grep, and 11 times faster than ripgrep. Both grep and ripgrep, being general purpose tools, will search the entire file, including the quality scores. Occassionally, targets will 'lurk' in quality scores, leading to false positives.

grepq also has a tune subcommand to analyze matched target strings and update the number and/or order of regex patterns in your pattern file according to their matched frequency. This can further speed up the filtering process.

Check out the tool and README here:

https://crates.io/crates/grepq

If you've downloaded a previous version, updating is as simple as:

cargo install grepq

grepq v.1.1.9 released today, bringing JSON support for pattern file input and tune subcommand output, allowing named regex sets and named regex patterns. gzip support was added in v.1.1.8

Check out grepq and README here:

https://crates.io/crates/grepq

I'm happy to release v.1.2.6 of grepq

Now supporting predicates for sequence header, minimum sequence length and minimum total quality score.

Crates.io https://crates.io/crates/grepq

Github https://github.com/Rbfinch/grepq

Free, open-source and built with Rust.

v.1.5.1of grepq now supports output of matched sequences to a SQLite database file, including GC content, tetranucleotide frequencies, and regex pattern matches and their position(s) in each matched FASTQ sequence, allowing for further analysis

Crates.io https://crates.io/crates/grepq

Github https://github.com/Rbfinch/grepq