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Old 12-22-2009, 01:50 AM   #1
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 203
Default Velvet de novo assembly of Solid reads HOWTO

Hi is there a more detailed howto do a de novo assembly with velvet?

I have looked at the SOLiD™ System de novo Accessory Tools
http://solidsoftwaretools.com/gf/project/denovo/

there is a cryptic reference to
List of programs/scripts included
This script belongs to the Velvet de novo assembly pipeline. Refer to Solid_denovo_HowTo for
more information on how to do de novo assembly of SOLiD™ reads.

but I can't find this particular howto. Anyone knows where it is?
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Old 01-10-2010, 01:11 AM   #2
kopi-o
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Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

I don't know where that howto is, but basically you just use Velvet. Before you do that, you're supposed to run the solid_denovo_preprocessor.pl script on your reads; there is a brief documentation file for that. Then you run Velvet on the resulting double-encoded file. After that, you run the solid_denovo_postprocessor.pl.

This blog post shows some sample commands that you might issue:

http://kevin-gattaca.blogspot.com/20...lid-reads.html


Quote:
Originally Posted by KevinLam View Post
Hi is there a more detailed howto do a de novo assembly with velvet?

I have looked at the SOLiD™ System de novo Accessory Tools
http://solidsoftwaretools.com/gf/project/denovo/

there is a cryptic reference to
List of programs/scripts included
This script belongs to the Velvet de novo assembly pipeline. Refer to Solid_denovo_HowTo for
more information on how to do de novo assembly of SOLiD™ reads.

but I can't find this particular howto. Anyone knows where it is?
kopi-o is offline   Reply With Quote
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