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.