abyss-pe contigs only

Question

[Siva]

Hello,

I'm using Abyss the first time to have contigs from pe and se reads so my command line is:

abyss-pe contigs stats clean name=UNmappedR k=60 j=9 in='unmappedPEandSE.fq'

I expected to have contig file only but got scaffolds also, is it normal?

Advance thanks,

Siva

Answer 1

[benv]

I think the 'stats' target is triggering the scaffold stage in an unexpected manner.

Possible workarounds:

(i) Leave the 'stats' target out of your abyss-pe command and just run 'abyss-fac' manually on the contigs file.

(ii) Try explicitly setting mp to empty, by adding mp='' to the abyss-pe command line.

You can add the --dry-run option to see what commands will be run by abyss-pe, without actually running them. It is a really handy option for troubleshooting.

[Siva]

ha good, without stats option unitigs file isn't created, only contigs are there :)

Answer 2

[Damian Kao]

Abyss will go through the entire unitig-contig-scaffold process. You should also have a .unitig and .contig file as one of your intermediate outputs.

[Siva]

yea also have unitgs, but if Abyss runs entire unitig-contig-scaf, these commands are just useless !?