https://github.com/audy/cd-hit-that

https://github.com/audy/cd-hit-that

Last synced: about 21 hours ago
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• Host: GitHub
• URL: https://github.com/audy/cd-hit-that
• Owner: audy
• Created: 2011-02-12T02:10:53.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2011-08-02T20:33:51.000Z (about 13 years ago)
• Last Synced: 2023-03-11T01:20:52.326Z (over 1 year ago)
• Language: Python
• Homepage:
• Size: 137 KB
• Stars: 2
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: readme.md

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README

        
# CD-HIT That

- Run CDHIT on a buncha files. Oh yeah, they're paired-end 

- Create a table of sequences per cluster per file

- Input data is paired-end, interleaved, FASTA reads which are joined together with their 5' ends touching and clustered.

# Usage:

- Reads go in `data/` and have to be in FASTA format

- Filenames need to have a number in them between a `_` and `.`. For example: `reads_blah_blah_033.fasta`. This is for the column header in the output table (it will be `33`). It goes without saying that this number should be unique.

To change parameters such has similarity requirement, edit the Rakefile.

The table will be saved as `counts.txt`

Type `rake clean` to start over.