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Old 04-16-2018, 05:32 AM   #1
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Location: Spain

Join Date: Mar 2018
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Default velvetg coverage parameter

Hi everyone, I am new with Velvet and I have some questions regarding velvetg parameters.

I am doing the de novo assembly for my Illumia 101 bp PE reads (HiSeq 4000), with a depth sequencing of 90 millions of reads per sample. The inserte size of my libraries is of 300 bp, so i have adjust the next parameters to:
-min_contig_lgth 350 -ins_length 300
Is that correct?

Regarding coverage, as the depth sequencing is high (90 M), I was thinking of setting a mínimum coverage value to avoid sequencing errors, but at the same time I do not want to lose information, so I am not sure how to fix this parameter. Is this parameter set with the –cov_cutoff option? As i don’t know the expected coverage of unique regions, should I add –exp_cov auto to my options?

I would enormously appreciate you suggestions!!
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