Hi Dan,
When the reorderer module runs, it creates a series of folders called
alignmentN inside the chosen output location. These contain successive
runs of the reordering algorithm, which continues either until the
contig ordering converges or a defined limit on the number of iterations
is reached.
Inside each of those alignmentN subfolders is a contigs fasta file that
contains the reordered contigs produced at that iteration. It sounds
like that is the file you're seeking, so no need to do any further
processing/export.
Best,
-Aaron
On Mon, 2016-04-11 at 16:38 -0400, Daniel Evans wrote:
> I am a student at the University of Pittsburgh who is trying to export
> a multiple-contig genome sequence from Mauve into a .gbk, .fasta, or
> other file type that can be used for annotation.
>
>
> I reordered the contigs of our sequence to match a reference sequence
> but haven't been able to export (or copy) this reordered sequence for
> further study. Is there a function in Mauve that would accomplish
> this?
>
>
> Thanks,
>
>
> Dan Evans
> University of Pittsburgh
> Department of Microbiology and Molecular Genetics
>
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Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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