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Old 07-12-2011, 07:50 AM   #1
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Location: texas

Join Date: Feb 2011
Posts: 5
Default how to resolve repeat areas with Velvet when doing de novo assembly

I am sequencing a bacterial genome and have assembled my Illumina reads (40 bp single) using Velvet. I am particularly interested in a particular gene (my gene of interest, MGIS) along with its neighboring genes that is probably located on a low copy number plasmid. One complicating factor is that MGIS is flanked by two genes that are repeated in the genome. I have tried to optimize parameters (k mer length, no gaps allowed, no mismatches allowed) in Velvet, and thus far, the largest contig that contains MGIS is only about 4 kb.
1. Are there any other parameters that I can change that may help to increase my contig size?
2. I have about 6 kb of sequence from MGIS and it flanking regions obtained from manual sequencing. Can I use this as a ‘reference’ to make Velvet or any other assembly program begin the assembly from this point and work outwards from this point to reassemble as much of the region as possible? I believe that I have enough read coverage, but I am guessing that because of the way that the assembly is working, the reads are being sequestered?

If anyone has any suggestions on some alternative approaches to reconstructing the plasmid based on the existing Illumina data, I would very much like to hear them.
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Old 10-24-2011, 09:42 PM   #2
Location: Pune, India

Join Date: Sep 2009
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May be you can the optimize "-exp-cov" and "-cov_cutoff" , also a higher value of K may help you to resolve the repeat structure.
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