[khmer] khmer/khmer-protocols confusion
Michael R. Crusoe
mcrusoe at msu.edu
Mon Feb 24 09:07:11 PST 2014
On Mon, Feb 24, 2014 at 10:58 AM, Francesco Rubino [frr11] <frr11 at aber.ac.uk
> Hello all,
Thank you for using the khmer suite and for your questions.
> 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?
The official GitHub repository for khmer is https://github.com/ged-lab/khmer.
The latest current release is v0.7.1. Our primary method for distribution
is via the Python Package Index ( https://pypi.python.org/pypi/khmer )
using the `pip` command as documented in
GitHub will present any branch or tag as a release. Titus's personal
repository has a branch named "protocols-v0.8.3" in reference to the
version of khmer-protocols not of the khmer project itself.
> 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.
That would be our error. Supporting the new format is being tracked in this
GitHub issue: https://github.com/ged-lab/khmer/issues/23
What document where you looking at?
> Francesco Rubino
> khmer mailing list
> khmer at lists.idyll.org
Michael R. Crusoe: Programmer & Bioinformatician mcrusoe at msu.edu
@ the Genomics, Evolution, and Development lab; Michigan State U
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