velvetg exp_cov?

[Tom_C]

Hello all,

I am very new to sequence analysis and am currently trying to teach myself how to assemble a bacterial genome from scratch. I am primarily a wet bench scientist with ZERO computer background, and the university I work at has no bioinformatics resources. Although I have poured over the manual and seqanswers for information, I still cannot grasp how to determine the exp_cov for velvetg. Can anyone provide some clarity? Thanks.

[Brian Bushnell]

Calculate (read_length x number_of_reads)/(expected genome size).

If you don't know the expected genome size, you can estimate it with kmers. For example, with BBTools, there is a program called khist.sh that will produce a histogram of kmer frequencies; the expected coverage would be the position of the first major peak. But you don't really need to; you can run Velvet without setting that flag.