[mira_talk] Re: --highlyrepetitive vs normal
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 13 Oct 2012 23:41:18 +0200
On Oct 13, 2012, at 17:29 , Juan Daniel Montenegro Cabrera wrote:
> I can see that I was overriding some of the changes of the flag with another
> parameters. When would you consider a assembly "higlyrepetitive"?, does it
> depend on the k-mer distribution? Do you have a treshold for it, would you
> recommend one?
Beside prior knowledge of the bug and what comes out of a draft assembly, the
kmer distribution is something I am also looking at. I haven't really worked
out a rule for the kmer distribution pattern, I just know what to expect from
prokaryotes or lower eukaryotes. Things are also complicated by the sequencing
technology / technologies used (Sanger, 454, Illumina or Ion) as well as
whether it's a hybrid; or may have plasmids / mitochandria / plastids; or
whether some data quality algorithms of MIRA are on or off.
Sorry :-)
B.
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