[mira_talk] fosmid assembly using mira
- From: Rohit Ghai <ghai.rohit@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 22 Dec 2009 18:42:40 +0100
Hi
I have a set of 40 fosmids that we sequenced using 454 (~70,000 reads). So
the 454 sequences also contain
our vector's sequence. I also have the fosmid end sequences for each of the
fosmids done previously
using Sanger ( only fasta files though ). The length of the fosmids is
typically within the range of 30-40kb.
Is it possible to use the fosmid end sequences with a distance constraint as
part of the assembly
( something like paired end reads ) in mira ? Since the fosmids are not
necessarily from a single
genome, I don't want them to be assembled as a complete genome so I'm
guessing the option -AS:use_genomic_pathfinder
should be off ( even though the -job switch contains genome ). However, its
not clear to me how I can
specify the file containing the ssaha results against the 454 dataset. Could
you suggest some
starting command lines that I can use to begin this assembly ?
thanks in advance
Rohit
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