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Old 04-26-2013, 08:12 PM   #1
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Location: Los Angeles, CA

Join Date: Aug 2011
Posts: 2
Default Finding contig repeat counts by mapping contigs to the reference genome

Hi guys, I have a set of contigs of genome G (using de novo assembly by Velvet) and I also have the complete sequence of the reference genome G. I want to know the repeat count (an integer number) of each contig in the reality by mapping them to the reference genome and finding and counting exact matches.

Which tools are easier to use? At the moment I'm just interested to have a 2 column result, one column showing the contig names and the other showing an integer number which is the repeat count of that contig in the reference genome. Everything else is just a bonus. Would you please let me know which tool is better or how I can easily produce this result based on MUMmer or BLAST output?

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