[cemi] Two (ok, three) quick points -- prokka, and read handling, and multiple files

[C. Titus Brown]

Hi all,

If you're running prokka on a metagenome, use '--metagenome' at the end of the command line.  That will find fragmented genes as well as full genes.  Run 'prokka' if you want to see the full set of options.

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Second, if you've got additional read handling concerns (like, splitting already-interleaved files) there is a set of documentation here that might help:

http://khmer.readthedocs.org/en/latest/scripts.html

See the read handling scripts specifically:

http://khmer.readthedocs.org/en/latest/scripts.html#scripts-read-handling

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And, finally, if you have more than one set of read files to assemble, we're working on protocols that will help you do that; see:

https://khmer-protocols.readthedocs.org/en/v0.8.2/

The mRNAseq quality control stuff is more mature than the metagenomic protocol:

https://khmer-protocols.readthedocs.org/en/v0.8.2/mrnaseq/index.html

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--titus