[mira_talk] EST assembly from polyploids
- From: "Schafleitner, Roland (CIP)" <R.SCHAFLEITNER@xxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 22 Apr 2009 10:05:20 -0500
Dear Bastien,
Congratulations for Mira, for its "biologist"-friendly use and
versatility.
My question is related to assembling Sanger and 454-generated ESTs of a
polyploidy crop (sweetpotato). While MIRA assembles ESTs derived from
one cultivar to very meaningful contigs, it has the tendency to produce
a lot (hundreds) of different contigs from ESTs that are highly abundant
in non-normalized libraries of different genotypes, instead of grouping
these ESTs into ~ 10 contigs, which would represent the number of loci I
would expect for this gene family. Sweetpotato sequences have a high
rate of polymorphisms and the amount of SNPs present in the ESTs might
be responsible for this result.
We have played around with the switches and got best result using the
-highlyrepetitive switch, but still we get, beside a lot of very
meaningful contigs, too many contigs for some gene families.
Would you have an idea how to modify the switches in order to mitigate
the effect of many SNPs in large EST clusters without lowering the
resolution of contig assembly from less abundant ESTs?
Thanks a lot,
R
Roland Schafleitner
PhD, Biotechnology Research Scientist
Germplasm Improvement and Crop Enhancement Division
International Potato Center - CIP
Avenida La Molina 1895, Apartado 1558
La Molina, Lima 12, Peru
Tel.: +51 (0) 1 349 6017, annex 3065
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