Soap de novo trans parameters

RyNkA · 01-08-2014, 02:09 AM

Hi all,

I just recently trying to use SOAP denovo-trans for de novo assembly of a non-model species. I did try to run SOAP-trans but i'm kind of confuse about the options in the config file.
---------------
3) asm_flags
This indicator decides in which part(s) the reads are used. It takes value 1(only contig assembly), 2 (only scaffold assembly), 3(both contig and scaffold assembly).
---------------

Which to choose in my case ? I have single end reads file, with read length ranging from 30-300

Any suggestions

jebowers · 01-08-2014, 12:12 PM

Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.

RyNkA · 01-08-2014, 05:56 PM

Quote:

Originally Posted by jebowers

Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.

Thanks for the answer.

That's what i was doubt about, what if i specify 3 ? What will the program behave, will it just omit scaffoldings step ?

jebowers · 01-09-2014, 07:45 AM

Yes the scaffolding step will happen or not, but it will only look at zero paired ends so I expect it should not take long to run.

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01-08-2014, 02:09 AM	#1
RyNkA Member Location: Brisbane Join Date: Jul 2013 Posts: 20	Soap de novo trans parameters Hi all, I just recently trying to use SOAP denovo-trans for de novo assembly of a non-model species. I did try to run SOAP-trans but i'm kind of confuse about the options in the config file. --------------- 3) asm_flags This indicator decides in which part(s) the reads are used. It takes value 1(only contig assembly), 2 (only scaffold assembly), 3(both contig and scaffold assembly). --------------- Which to choose in my case ? I have single end reads file, with read length ranging from 30-300 Any suggestions

01-08-2014, 12:12 PM	#2
jebowers Member Location: Athens, GA, USA Join Date: Apr 2013 Posts: 19	Without paired end reads you will only be able to construct contigs (not scaffolds). You can either specify 1 or 3.

01-09-2014, 07:45 AM	#4
jebowers Member Location: Athens, GA, USA Join Date: Apr 2013 Posts: 19	Yes the scaffolding step will happen or not, but it will only look at zero paired ends so I expect it should not take long to run.