[mira_talk] Re: MIRA used for the German E. coli outbreak analysis
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 1 Aug 2011 11:50:58 +0200
On Monday 01 August 2011 11:26:59 Lionel Guy wrote:
> In case you missed it, Karch et al. used MIRA to assemble (by reference and
> de novo) IonTorrent reads from the E. coli outbreak strain, and from a
> historical related strain. I had a look at the reads from the first
> strain, and I'm not convinced by the quality yet. Searching for SNPs, it
> requires to ignore any homopolymer with length > 3 if you want to avoid
> errors.
Oh, had not seen that paper, nice. Current IonTorrent data indeed very much
feels like the first 454 GS20 data from early 2005/2006: problems with
homopolymers all over the place. However, 454 was able to crank up quality to
current levels within something like 12 to 18 months, I have some hope that
Ion will be able to do that also.
> And even in the shorter homopolymers, there are some errors that
> are obvious. They say that after the mapping assembly, they had to correct
> manually 51 out of the 1144 "core" genes, (~5%), which is not impressive.
Yep, I would not want to use Ion data without complementing it with Solexas,
which with current Ion lengtzh of ~100bp is a somewhat futile exercise. But as
soon as Ion gets their reads in the 250 bp range things become interesting
again from read length perspective if Illumina stays <= 150bp.
> BTW, in my opinion, they got the MIRA citation wrong (Genome Res 2004
> paper).
Cannot really blame them for that: it's the only MIRA paper in a journal
(admittedly high-ranking). The other "more-or-less-paper" is from the GCB 99
conference and is not indexed by PubMed. But as "Bioinformatics" reviewers
somehow always rejected papers I submitted on MIRA or specific algorithms, I
prefer to spend my spare time by developing MIRA instead of chasing wild goose
and some cranky ideas of reviewers. Whether or not a new paper on MIRA will
appear is pretty uncertain :-)
B.
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