[khmer] Dealing with paired-End Data (Alexis Groppi)

[Torsten Seemann]

(thank you Adina for the thorough reply!)

If you're focused on scaffolding and longer assemblies in general, maybe
> you want to prioritize the retention of your paired ends. If you're having
> trouble completing assemblies at all, you might try discarding more data at
> the cost of paired ends.
>

One way to get some of the advantages of both is to try and sequence an
overlapping paired-end library. For example, if you have a fragment size of
250bp and you sequence 2 x 150bp, then you end up with about half your
reads overlapping (which can be joined into lovely ~250bp single end reads)
and other half remaining as paired-end reads. I then use the SE reads for
diginorm (sorted by longest first) and experiment/explore with those. If
needed, I then consider incorporating the PE reads. Assembly algorithms
tend to be happier with SE reads only, and the longer the better. PE reads
can be useful for longer range information, but they make assembly more
difficult.

-- 
*--Dr Torsten Seemann
--Scientific Director : Victorian Bioinformatics Consortium, Monash
University, AUSTRALIA*
*--Senior Researcher : VLSCI Life Sciences Computation Centre, Parkville,
AUSTRALIA
--http://www.bioinformatics.net.au/*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20130326/0d389c2f/attachment-0002.htm>