[khmer] khmer/khmer-protocols confusion

Francesco Rubino [frr11] frr11 at aber.ac.uk
Mon Feb 24 07:58:47 PST 2014

Hello all,

I've read part of the documentation of khmer and I'm interested in using it to either partition or normalise a meta-transcriptome I have. I have a bit of confusion about the versions of the software, though. I have a few questions I hope you can answer:

1) I've read both about a khmer 0.7.x (http://khmer.readthedocs.org/en/latest/) and a 0.8.x (https://github.com/ctb/khmer/releases). Which should I use?
2) I see in the documentation that you need to interleave the fastq files if using paired-end data. Why do you refer as "@name/1" as the new casava format? I thought that one is the old one.

Francesco Rubino
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