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

[Akshaya R. <ar...@bu...>]

Ah beautiful! I did eventually get amos installed, but these are much
better options.
Thank you so much,
Akshaya

On Sat, Oct 11, 2014 at 3:53 PM, Brian Walenz <th...@gm...> wrote:

> 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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>


-- 
Akshaya Ramesh
PhD candidate
Kepler Lab
Laboratory of Computational Immunology
Boston University School of Medicine
72 E Concord Street, Room 504D
Boston, MA 02118