Contigs rearrangement

[Rachel]

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

[boetsie]

Hi Rachel,

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

See this thread for SSPACE:

http://seqanswers.com/forums/showthread.php?t=8350&highlight=SSPACE

For Bambus see;

http://sourceforge.net/apps/mediawiki/amos/index.php?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

[Thorondor]

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/

[boetsie]

I don't think the contigs can be arranged into scaffolds with those two programs...

[Thorondor]

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.