[protocols] velvet assembly after partitioning with khmer

[C. Titus Brown]

Hi Stuart,

what's the command line you were running when you got the error?

thanks,
--titus

On Tue, Jun 03, 2014 at 04:10:02PM -0400, Stuart Jones wrote:
> Hello,
> First, thanks so much for khmer and the protocols you have provided!  I am attempting to assemble the genome of a methanogen from paired-end MiSeq data generated from an enrichment culture.  I worked through the metagenome assembly protocol and was able to generate compressed PE and SE group files, but did not run the reinflating partitions steps.  After this, I attempted to assemble one of the PE and SE group files using Velvet and got an error I haven't seen from Velvet before:
> ">> Please re-order the filenames in yoru command line so as to have the reference sequence files before all the others"
> 
> Seen this before?
> 
> Thanks,
> Stuart
> 
> Stuart E. Jones
> Assistant Professor
> University of Notre Dame
> Dept. of Biological Sciences
> 264 Galvin Life Sciences
> Notre Dame, IN 46556
> sjones20 at nd.edu
> (574) 631-5703
> 
> 
> 
> 
> 
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-- 
C. Titus Brown, ctb at msu.edu