[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
> wrote:

>  Hello all,

Hello Francesco,

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?

>  Thanks,
>  Francesco Rubino
> _______________________________________________
> khmer mailing list
> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer

Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
http://ged.msu.edu/ http://orcid.org/0000-0002-2961-9670
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