Soap de novo trans parameters

[RyNkA]

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

Any suggestions

[jebowers]

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

[RyNkA]

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]

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.