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Old 08-23-2018, 09:35 PM   #1
bioramg
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Location: South Korea

Join Date: Apr 2014
Posts: 2
Wink How to set cutoff coverage and expected coverage

Hi all,
I am new to mitochondrial genome assembly using whole genome sequencing. I tried to assemble with velvet with different k-mers, expected coverage - auto and coverage cutoff as auto. But I got contigs which is >97% similarity with chloroplast genomes. So, I read that I have to optimize both cutoff value or coverage. So, could you please which command I should use for velvet to optimize both cutoff coverage and expected coverage values? Whether I should use both velveth and velvetg or velvetoptimiser? I am very beginner in Ubuntu commands. So, please help me in this regards,
Thank you.
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denova assembly, illumina, velvet

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