[mira_talk] MIRA used for the German E. coli outbreak analysis
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 1 Aug 2011 11:26:59 +0200
Dear MIRAists,
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. 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.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022751
BTW, in my opinion, they got the MIRA citation wrong (Genome Res 2004 paper).
Cheers,
Lionel
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