[khmer] less reads but more kmers?

[Nacho Caballero]

That makes a lot of sense, thanks!


On Sat, Jan 18, 2014 at 10:50 AM, C. Titus Brown <ctb at msu.edu> wrote:

> On Sat, Jan 18, 2014 at 05:00:03AM -0800, C. Titus Brown wrote:
> > On Fri, Jan 17, 2014 at 09:31:32PM -0200, Nacho Caballero wrote:
> > > I used khmer to digitally normalize two assemblies:
> > >
> > >    - After normalization, Assembly A has *1.5 million reads*, and
> during
> > >    assembly SPAdes uses *116 million* kmers (k=37)
> > >    - After normalization, Assembly B has *1.5 million reads*, during
> > >    assembly SPAdes uses *612 million* kmers (k=37)
> > >
> > > I followed the same protocol on both assemblies (quality filtering with
> > > Trimmomatic, 3-pass normalization, etc.), so I don???t understand why
> > > assembly B, with 16x fewer reads, has 8x more kmers than assembly A.
> > >
> > > What are some possible explanations?
> >
> > Barring some extraordinarily bizarre bug, the answer *must* be SPAdes
> > is *choosing to use* more k-mers... I'll ask the SPAdes authors ;)
>
> Anton (one of the SPAdes authors) pointed out that I'd misread the e-mail.
> If dataset A and dataset B are from different samples, then they could
> easily
> have different levels of diversity which would lead to different numbers of
> k-mers for the same coverage level.
>
> The simplest explanation would be that dataset B is both more diverse
> and has lower coverage than dataset A, I think.  I would guess that
> if you generated 6 times as much data for sample B then diginorm would
> leave you with many more reads, although this is a bit dependent on the
> diversity of sample B.
>
> cheers,
> --titus
>
> >
> > If you want to check the total number of k-mers, we have some scripts
> > in khmer to do that.  See 'abundance-dist-single.py' here,
> >
> >
> http://khmer.readthedocs.org/en/latest/scripts.html#scripts-counting
> >
> > cheers,
> > --titus
> > --
> > C. Titus Brown, ctb at msu.edu
> >
> > _______________________________________________
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>
> --
> C. Titus Brown, ctb at msu.edu
>
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