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Old 03-07-2011, 08:29 PM   #1
Rachel
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Question Contigs rearrangement

Hi

I am having 2x100 PE reads from Illumina. I assembled the reads by de novo and obtained alot of contigs. May I know what is the recommended software to arrange the contigs into a scaffold?

Thanks
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Old 03-08-2011, 05:13 AM   #2
boetsie
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Hi Rachel,

two most common tools used are SSPACE (developed by me) and Bambus.

See this thread for SSPACE:
http://seqanswers.com/forums/showthr...ghlight=SSPACE

For Bambus see;
http://sourceforge.net/apps/mediawik...p?title=Bambus

Though with Bambus i think you should have modifications to your input data, which you do not need with SSPACE.

Kind regards,
Boetsie
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Old 03-08-2011, 08:33 AM   #3
Thorondor
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if it is DNA take a look at velvet:
http://www.ebi.ac.uk/~zerbino/velvet/

if it is mRNA maybe you want to try out oases:
http://www.ebi.ac.uk/~zerbino/oases/
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Old 03-08-2011, 08:45 AM   #4
boetsie
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I don't think the contigs can be arranged into scaffolds with those two programs...
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Old 03-08-2011, 09:01 AM   #5
Thorondor
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well, he can redo the assembly with only the reads or also input the contigs he got so far with -long and turn scaffolding on. He will need the PE reads anyway.
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