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Old 01-06-2016, 06:24 AM   #1
Haumich
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Location: Israel

Join Date: Jul 2015
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Default deNovo/merged genome to big

Hello Everyone,

in my project, I deNovo-assembled a genome of a non-model rodent using "Abyss". I now have various scaffolds, which I merged, using "GAM-NGS". I know that the genome is about 3 billion bp long. The merged genome(s) however, are much longer, some about 3.8 billion bp.
I already filtered out all scaffolds smaller than 1000 bp, which is the average length of a gene for this species. Can I naively throw out the smallest scaffolds until I reach ~3 billion bp, or do I have to tweak the merging process?
My usual way of determining the quality of an assembled genome is mapping back DNA/RNA-Seq data and look at the mapping rate, but this obviously favors larger genomes.
I would appreciate if someone could share his/her experience here.
Thanks
Robert

Update: I tested various assemblers, but Abyss performed best. I am merging assemblies for different Kmers, which is recommended in literature.

Last edited by Haumich; 01-09-2016 at 09:38 PM.
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Old 01-06-2016, 07:16 AM   #2
mastal
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Default

You only mention Abyss. I haven't used GAM-NGS, but I thought the idea was to merge assemblies produced by different assemblers. I would try one or more other assemblers to see how different the assemblies they give are.
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