Need help on soap denovo
 

Hi all, :confused:

Currently i'm running soapdenovo . i am getting two output files one is (1).contig , and the second one is (2).scafseq as per their mentioned in that webpage. But i need to view the result in "GUI" , like any of viewer (for ex: hawkeye , eagleview) .


It would be great if i get a positive reply for this

Thanks in advance.

Why do you need to view your contigs or scaffolds? As this is a de novo assembly, the only thing you get back are contigs or scaffolds. You can look at them in a special viewer, but you will see nothing more than just doing a "more" or to open them in a text editor...

hmmm ... your right..... But while i done with "velvet" denovo assembly .. I have got the .afg file ,so that i can easily shows the assembly files in the viewer (GUI) format. Like wise in abyss,edena . But while i go for soapdenovo i can get only .contig file in a text format. I Couldn't in view in a GUI ,eventhough i tried some converter like ".toAmos.pl" file to convert .contig to .afg or .ace , There is some problem in a converter..So i am fully confusing ,i couldn't find any of correct path ... it would be great,if i get a solution for this..

Thanks in advance

Soap de novo .afg file
 

Hello Sunder,

to get the.afg you need to tell SoapDeNovo to generate it. In other words you need to turn the amos_file switch on (beware..the .afg it's a LARGE file):

./velvetg output_directory/ -amos_file yes

Then you can have a look at it with Tablet or other viewers (beware #2: it will usually take quite a lot of time to generate the .afg output in the GUI viewer).

Hope it helps,
Rocco