SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Velvet de novo assembly to amosvalidate (http://seqanswers.com/forums/showthread.php?t=508)

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.

D

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?

Thanks,
Canuck

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?


All times are GMT -8. The time now is 05:58 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.