A couple Python-based FASTQ QC tools that perform several useful file handling operations, notably check read-pairing, repair read-pairing, and trim reads. Notably, fq-repair is the only tool (to my knowledge) that can successfully re-pair reads from gzipped FASTQ input. All tools are designed to be as fast and memory-efficient as possible. Input is assumed to be 4-line FASTQ and may be gzipped.

fqutils has no dependencies aside from the Python 3 standard library (if this Python is installed, things will work). Just clone the repository with with git clone https://github.com/jstaf/fqutils.git. Clever users will also note that this repository can be installed as a python package with pip install .

To run tests: pytest

Run commandname --help for individual usage instructions. Sample commands can also be found in the tests/ directory.

• fq-checkpair - Check if two FASTQ files are properly paired and highlight errors.

• fq-trim - Starting from both ends, trim a read so that bases below a certain Phred quality score are removed. Resulting reads shorter than a minimum length are removed. Fast, dirty, and idiot-proof trimming.

• fq-repair - Re-pair the reads in two FASTQ files if reads have been filtered out or otherwise reordered.

• fq-zwc - Just a wrapper around wc -l for gzipped files.