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Old 02-04-2015, 09:27 AM   #5
Location: Europe

Join Date: Mar 2014
Posts: 42

I used Velvet and Metavelvet to do the assemblies and kmergenie to find the coverage cut-off to use in the assembly. There were about 12 million reads that went into the assembly. My reads had lengths that were between 70-110bp long. I ended up using a coverage of 6, kmer length of 33 and insert length cut off of 400 plus I opted for scaffolding. This combination provided me with the longest contigs and N50 of 350bp which is the best that I could get.
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