sanger and solexa reads assemby

peio · 09-08-2009, 04:49 AM

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!!

lcollado · 09-08-2009, 09:57 AM

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

peio · 09-09-2009, 02:03 AM

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.

sklages · 09-09-2009, 02:25 AM

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

peio · 09-09-2009, 03:06 AM

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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09-08-2009, 04:49 AM	#1
peio Junior Member Location: Spain Join Date: Mar 2009 Posts: 6	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!!

09-08-2009, 09:57 AM	#2
lcollado Member Location: Baltimore, MD Join Date: Jun 2009 Posts: 65	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 __________________ L. Collado Torres, Ph.D. student in Biostatistics.

09-09-2009, 02:03 AM	#3
peio Junior Member Location: Spain Join Date: Mar 2009 Posts: 6	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.

09-09-2009, 02:25 AM	#4
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	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

09-09-2009, 03:06 AM	#5
peio Junior Member Location: Spain Join Date: Mar 2009 Posts: 6	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.