Has anyone in here used OPERA-LG or PBJelly to improve assembly by better scaffolding and filling in gaps ?
Actually I am seeking explanation to few "abnormalities" that I am not able to understand:
After running OPERA-LG (Paired end data + pacbio data), the max scaffold size increased and number of scaffolds decreased...but along with that neither the genome size increased nor the gaps were removed (rather they increased !!) with regard to the PE data assembly...what can possibly be the reason ??
With PBJelly run, first blasr never run from within the script and second even if all the stages execute succesfully, in the fifth and sixth stage it refuses to assemble the sequences at all (I can see all the files being present though !!!). I have manually checked that there are actually pacbio reads spanning the gaps in the scaffolds from PE data assembly by velvet.
Any help, opinion and suggestion is highly appreciated and thanks in advance.