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Old 09-23-2010, 03:06 PM   #1
jgibbons1
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Location: Worcester, MA

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Default ABySS contig coverage?

I've beebn playing around with ABySS and haven't been able to find much documentation on calculating contig coverage. The header to each contig reads as follows:

>13 1504 10278

Which I am assuming is:

>ID contig_length ???

I realize the 10278 isn't coverage, but what is it? And more importantly is there a way to calculate coverage?

Thanks,

John
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Old 09-23-2010, 10:22 PM   #2
natstreet
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It's probably worth posting this message to the ABySS google group as well http://groups.google.com/group/abyss-users

You should also see this old post http://www.bcgsc.ca/pipermail/abyss-...ch/000019.html

and here is another description of the contig headers http://seqanswers.com/wiki/ABySS

Last edited by natstreet; 09-23-2010 at 10:25 PM.
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Old 09-24-2010, 06:56 AM   #3
jgibbons1
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Very helpful...thanks natstreet!
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abyss, assembly, coverage, de novo, read length

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