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Old 09-05-2017, 01:45 AM   #1
splaisan
senior molecular biologist
 
Location: Belgium

Join Date: Jun 2009
Posts: 29
Default Method for comparing denovo to reference assembly

I obtained a non-sorted assembly (contigs) which I would like to:
* compare to the expected reference genome (available as fasta, gff, gbk)
* sort and re-orientate the contigs to best match the reference
* plot xy diagonal between the sorted and the ref
* generate AGP file describing the matches and gaps between the two

Can someone please propose best tools and ideally tutorial pages to do this.

So far I used nucmer+mummer-plot and mauve but they do not provide the AGP and plots are not so nice. I am confident there is better out there.

Thanks
Stephane
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assembly, denovo genome assembly, genome comparison

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