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Old 08-20-2008, 09:16 AM   #1
canuck
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Default Velvet de novo assembly to amosvalidate

Has anyone successfully put a Velvet de novo assembly (*.afg) file through amosvalidate? Specifically, GS FLX data without a reference genome?
I can't seem to generate a valid amos-bank (error: No library account found in bank). I hope I'm not missing the obvious.

Thanks for any pointers.
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Old 03-30-2009, 08:35 PM   #2
dlepp
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Default Velvet de novo assembly to amosvalidate

Also tried with no luck using .afg file produced from Solexa paired-end run. I was able to generate the bank and view it with Hawkeye, albeit painfully slowly, but ran into errors when running amosvalidate. Interested to know if you got it to work.

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Old 04-28-2009, 05:19 AM   #3
canuck
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Default Velvet de novo assembly to amosvalidate

No. I got only as far as you. Amosvalidate also failed for me. Sorry I haven't looked at this for quite a while and haven't tried anything further.

On another topic, do you know of any way to visually compare two assemblies simultaneously?

Thanks,
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Old 04-28-2009, 08:47 AM   #4
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How big are those assemblies / expected genomes?
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Old 04-28-2009, 09:49 AM   #5
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From my recollection, the genome size was 5Mbp (bacterial genome).
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Old 07-17-2011, 12:24 PM   #6
Irsan_Kooi
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I have tried to run amosvalidate on a bank made from a velvet.afg file as well, no luck yet.

Does anyone know how to perform the amosvalidate on a .bnk file derived from velvet_.afg file?
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