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        "author": "Jeff Stafford",
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        "description": "# fqutils\n\nA couple Python-based FASTQ QC tools that perform several useful file handling operations, \nnotably check read-pairing, repair read-pairing, and trim reads. \nNotably, `fq-repair` is the only tool (to my knowledge) \nthat can successfully re-pair reads from gzipped FASTQ input.\nAll tools are designed to be as fast and memory-efficient as possible.\nInput is assumed to be 4-line FASTQ and may be gzipped.\n\n## Installation and tests\n\n`fqutils` has no dependencies aside from the Python 3 standard library \n(if this Python is installed, things will work).\nJust clone the repository with with `git clone https://github.com/jstaf/fqutils.git`.\nClever users will also note that this repository can be installed as a python package with `pip install .`  \n\nTo run tests: `pytest`\n\n## Current scripts\n\nRun `commandname --help` for individual usage instructions.\nSample commands can also be found in the `tests/` directory.\n\n* **fq-checkpair** - Check if two FASTQ files are properly paired and highlight errors.\n\n* **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.\n\n* **fq-repair** - Re-pair the reads in two FASTQ files if reads have been filtered out or otherwise reordered. \n\n* **fq-zwc** - Just a wrapper around `wc -l` for gzipped files.\n",
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