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canuck 08-20-2008 09:16 AM

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.

dlepp 03-30-2009 08:35 PM

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.


canuck 04-28-2009 05:19 AM

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?


bioinfosm 04-28-2009 08:47 AM

How big are those assemblies / expected genomes?

canuck 04-28-2009 09:49 AM

From my recollection, the genome size was 5Mbp (bacterial genome).

Irsan_Kooi 07-17-2011 12:24 PM

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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