[mira_talk] misassembly problems

Dear all,

I assembled a really complicate microbial genomes full of IS (full I
mean really full). I found several, I think, misassembled reads. The
project is half-plate GS-FLX20 Paired-Ends assembly. No much complicated
for mira (less than 4h in accurate mode), these are the parameters:

mira -project=my_prj -job=denovo,accurate,454,genome -GE:not=2:kcim=yes
-SK:mnr=YES -AS:nop=12:rbl=6:sd=1

I decided to increase the 'nop' to 12 and 'rbl' to 6 whit the hope this
can improve my previous attempt I applied just using standard parameters
(accurate mode). In this attempt I also tried to use the 'kcim' and 'sd'
parameters (no problem whit memory, I have a 16Gb, 64bit machine whit
Ubuntu 8.10).

Go to the problem.
I found several contigs whit reads probably erroneously assembled (look
at the light-blue A at position 8430). I said misassembled because the
respective forward or reverse partner is in another contig and if I
disassemble and try to join again (manually) it make sense. The problem
is that this events causes wrong contigs whit big problem when I go to
Gap4 (people call it finishing .... ironic ???).
Can I fix parameters in order to avoid this kinds of errors in the
contigs, if yes which one?.
Please someone have information, suggestion, miracle (eheheh) for this
problem?

Thank you in advance,
have a nice day,

Giuseppe


-- 
Dr. Giuseppe D'Auria

Cavanilles Institute for
Biodiversity and Evolutionary Biology
University of Valencia
"Poligono de la Coma" s/n
46980 Paterna (Valencia),Spain

web: http://www.uv.es/cavanilles/genevol/
tel: +34 9635 43646

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