Velvet de novo assembly of Solid reads HOWTO

KevinLam · 12-22-2009, 01:50 AM

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 · 01-10-2010, 01:11 AM

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

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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12-22-2009, 01:50 AM	#1
KevinLam Senior Member Location: SEA Join Date: Nov 2009 Posts: 203	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?