So after one week of running, the output was really awful, with an N50 of 1 and the coverage was estimated as 6. Can you give me any input on how to better pick the kmer size? The output I get now from kmer genie seems to be too low but I don't know how much deviation from such histograms are allowable before the output becomes spurious.
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Try using velvetk.pl to calculate coverage first, you can get the script from:
http://www.vicbioinformatics.com/software.velvetk.shtmlComment
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In the following link, there is an explanation of evaluating kmer coverage using the stats.txt file generated by your first assembly:
Of course, I'm not certain how good the initial assembly has to be for this to be accurate.Comment
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