Re: [wgs-assembler-users] Viewing .asm files generated by Celera

[Brian W. <th...@gm...>]

Hi-

The .asm is unwieldy and terrible to parse.  Use the 'posmap' files,
specifically the frgctg or frgscf files list the position of each fragment
in a contig/scaffold.

http://wgs-assembler.sourceforge.net/wiki/index.php/POSMAP

Another option:

https://sourceforge.net/p/wgs-assembler/mailman/message/31494576/

b



On Mon, Oct 6, 2014 at 11:13 AM, Akshaya Ramesh <ar...@bu...> wrote:

> Dear All,
>
> I would like to get information on coverage and the reads that were used
> to form a contig/scaffold. Is it right to assume that the .asm file
> contains this information? And if it does, I was wondering what package you
> use to view these files?
>
> I have been working on installing amos3.1 which has a utility called
> hawkeye that can be used to view .asm files. However, I am unable to
> configure amos such that it recognizes CA files.I have sent an e-mail to
> the amos-help, posted in seqanswers (
> http://seqanswers.com/forums/showthread.php?t=47221) with no luck.
>
> Do any of you have any suggestions or have run into similar problems?
>
> I really appreciate your help.
> Best,
> Akshaya
> --
> Akshaya Ramesh
> PhD candidate
> Kepler Lab
> Laboratory of Computational Immunology
> Boston University School of Medicine
> 72 E Concord Street, Room 504D
> Boston, MA 02118
>
>
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