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Old 06-11-2015, 12:09 PM   #1
Location: Tempe, AZ

Join Date: Oct 2013
Posts: 11
Default re-scaffolding using BAC end read pairs


I have a vertebrate genome assembly with contigs and scaffolds generated from ~80X PE Illumina small-insert and mate-pair libraries. There are also some BAC scaffolds and a few thousand BAC Sanger reads available for this species in the GenBank Trace database. I would like to use these publicly available data to merge scaffolds and improve on the Illumina-only assembly.

Aligning the assembled BAC scaffolds to the original genome scaffolds and generating consensus sequences to merge contigs/scaffolds seems fairly straightforward, can anyone recommend a method/pipeline that has worked for them? This was mentioned once here

I assume I can use the BAC end paired sequences with a scaffolding tool such as SSPACE ( ) but what is the best way to trim or at least incorporate quality scores? I don't think I want to simply use the raw traces downloaded from GenBank, unless anyone can convince me otherwise.

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bac, bac scaffold, scaffolding, sspace

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