[mira_talk] Re: Correct 454 errors with Solexa reads?
- From: Dan Bolser <dan.bolser@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 Dec 2009 09:01:43 +0000
2009/12/14 Björn Nystedt <bjorn.nystedt@xxxxxxxxx>:
> Hi all,
> we are doing a bacterial genome (2Mb) project where we have about 50X 454
> coverage (plus some Sanger data from fosmids and PCRs for gap-closure). The
> genome is more or less complete, but still we have problems with 454
> homopolymer errors causing frameshifts. We have now run Solexa sequenceing
> (120X; yepp we got more data than expected) on the same genome to correct
> those frameshifts. We are now trying different strategies of combining our
> data to get the highest possible quality in the shortest possible time.
> Things are looking pretty good allready so I am not too worried, but I wanted
> to ask if anyone has any experience of this? Strategies we are considering are
>
> mapping Solexa with MIRA to a fasta backbone
> mapping Solexa with MIRA to a caf backbone
> de-novo assembly with MIRA, using all data (including fake 20kb overlapping
> reads to avoid messing up the original assembly) (slow!)
> mapping Solexa with another software BWA/SOAP2/RMAP/Bowtie to a fasta backbone
> de-novo assembly with Velvet, using all data (not so slow)
>
> So far we have run the mapping in MIRA to a fasta backbone, wich works quite
> nice but not perfectly (see previous discussion on the list 'Alignment errors
> in Solexa mapping').
>
> Happy for any ideas/comments!
I'm not an expert by any means, but I heard that people like the MAQ
SNP calling pipeline. If you map your solexa reads to your 454
assembly using MAQ, errors in homopolymer run length should be called
as INDELS... I think...
Some kind of INDEL calling mapper should do the trick.
You could check if something is listed here (or not):
http://seqanswers.com/wiki/Special:BrowseData
> Björn
>
>
>
>
>
> ====================================
> Björn Nystedt, PhD
> Molecular Evolution
> EBC, Uppsala University
> Norbyv. 18C, 752 36 Uppsala
> Sweden
> phone: +46 (0)18-471 45 88
> email: Bjorn.Nystedt@xxxxxxxxx
> ====================================
>
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