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Old 09-08-2009, 04:49 AM   #1
peio
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Default sanger and solexa reads assemby

Hi,
We'd like to assembly sanger and solexa reads together against a reference transcriptome.
I have look for an application to do that and I only found mira. Unfortunately We can not use it due to its high memory requirements.

Is there any other app to do that.
thanks!!
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Old 09-08-2009, 09:57 AM   #2
lcollado
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I haven't done this before, but you can probably try using Velvet with the -long argument. Check the manual and the arguments for velveth

Leo
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Old 09-09-2009, 02:03 AM   #3
peio
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I heva looked at the velvet mailing list and unfortunately I have found that velvet doesn't work properly for this kind of hybrid assemblies.
Thanks for the answer!
p.
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Old 09-09-2009, 02:25 AM   #4
sklages
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You have a reference transcriptome ... mapping shouldn't be too hard (for any software). Have you tried MIRA? What machine you are running your assemblies?

cheers,
Sven
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Old 09-09-2009, 03:06 AM   #5
peio
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Our first choice have been Mira. But memory requirements are to high. We can't give to mira all our reads (solexa and sanger).
Now, our strategy is to group reads by alignments to reference and then give the groups to mira.
p.
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