https://github.com/kdm9/knives
A pipelined quality control script that utilises the UC Davis Biocore's sabre, sickle, scythe and seqqs.
https://github.com/kdm9/knives
Last synced: about 2 months ago
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A pipelined quality control script that utilises the UC Davis Biocore's sabre, sickle, scythe and seqqs.
- Host: GitHub
- URL: https://github.com/kdm9/knives
- Owner: kdm9
- License: mit
- Created: 2014-04-28T04:13:17.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2014-07-28T12:06:24.000Z (almost 11 years ago)
- Last Synced: 2025-02-14T21:47:10.887Z (4 months ago)
- Language: Python
- Size: 875 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
knives
======
A pipelined quality control script that utilises the UC Davis Bioinformatics
Core's [sickle](https://github.com/najoshi/sickle),
[scythe](https://github.com/vsbuffalo/scythe) and
[seqqs](https://github.com/vsbuffalo/seqqs).
Usage:
------
Knives takes paired input FASTQ files, and outputs paired good quality reads,
and single reads whose pairs failed quality control. It also takes a range of
mandatory and optional parameters. Run
$ knives
to see a full range of parameters. A detailed user manual is on it's way, but
as this tool is simply a wrapper around
[sickle](https://github.com/najoshi/sickle),
[scythe](https://github.com/vsbuffalo/scythe) and
[seqqs](https://github.com/vsbuffalo/seqqs), one can for the time being consult
their excellent user guides, available from each tool's GitHub page.