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: 11 days 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 (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-07-28T12:06:24.000Z (over 10 years ago)
• Last Synced: 2024-10-11T19:22:58.880Z (about 1 month 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.