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sklages · 05-20-2009, 07:36 AM

Maybe it's a good idea to get the latest cap3 binary for your platform at http://seq.cs.iastate.edu/

If you want to cluster before assembling you could try wcd (http://code.google.com/p/wcdest/) which makes a good job on clustering our data.

You can also use (for assembling your transcriptome dataset) MIRA2 assembler, http://chevreux.org/projects_mira.html

We ran into problems with TGICL with 454 data with very deep clusters (the clustering itself crashed, not the subsequent assembly). The author doesn't recommend TGICL for big NGS datasets.

hth,
Sven

05-20-2009, 07:36 AM	#5
sklages Senior Member Location: Berlin, DE Join Date: May 2008 Posts: 628	Maybe it's a good idea to get the latest cap3 binary for your platform at http://seq.cs.iastate.edu/ If you want to cluster before assembling you could try wcd (http://code.google.com/p/wcdest/) which makes a good job on clustering our data. You can also use (for assembling your transcriptome dataset) MIRA2 assembler, http://chevreux.org/projects_mira.html We ran into problems with TGICL with 454 data with very deep clusters (the clustering itself crashed, not the subsequent assembly). The author doesn't recommend TGICL for big NGS datasets. hth, Sven