[mira_talk] Correct 454 errors with Solexa reads?
- From: Björn Nystedt <bjorn.nystedt@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 14 Dec 2009 08:56:35 +0100
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!
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
====================================
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
