<div dir="ltr"><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Feb 24, 2014 at 10:58 AM, Francesco Rubino [frr11] <span dir="ltr"><<a href="mailto:frr11@aber.ac.uk" target="_blank">frr11@aber.ac.uk</a>></span> wrote:<br>
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Hello all,</div></div></blockquote><div><br></div><div>Hello Francesco,</div><div><br></div><div>Thank you for using the khmer suite and for your questions.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<div>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:<br>
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<div>1) I've read both about a khmer 0.7.x (<a href="http://khmer.readthedocs.org/en/latest/" target="_blank">http://khmer.readthedocs.org/en/latest/</a>) and a 0.8.x (<a href="https://github.com/ctb/khmer/releases" target="_blank">https://github.com/ctb/khmer/releases</a>). Which should I use?<br>
</div></div></div></blockquote><div><br></div><div>The official GitHub repository for khmer is <a href="https://github.com/ged-lab/khmer">https://github.com/ged-lab/khmer</a>. The latest current release is v0.7.1. Our primary method for distribution is via the Python Package Index ( <a href="https://pypi.python.org/pypi/khmer">https://pypi.python.org/pypi/khmer</a> ) using the `pip` command as documented in <a href="http://khmer.readthedocs.org/en/latest/">http://khmer.readthedocs.org/en/latest/</a></div>
<div><br></div><div>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.</div>
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<div>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.<br></div></div>
</div></blockquote><div><br></div><div>That would be our error. Supporting the new format is being tracked in this GitHub issue: <a href="https://github.com/ged-lab/khmer/issues/23">https://github.com/ged-lab/khmer/issues/23</a></div>
<div><br></div><div>What document where you looking at?</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<div>Thanks,<br>
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<div>Francesco Rubino<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><span style="font-family:'courier new',monospace;font-size:small">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">mcrusoe@msu.edu</a><br style="font-family:'courier new',monospace;font-size:small">
<span style="font-family:'courier new',monospace;font-size:small"> @ the Genomics, Evolution, and Development lab; Michigan State U</span><br style="font-family:'courier new',monospace;font-size:small"><a href="http://ged.msu.edu/" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://ged.msu.edu/</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://orcid.org/0000-0002-2961-9670" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://orcid.org/0000-0002-2961-9670</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://twitter.com/biocrusoe" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">@biocrusoe</a><br>
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