MaSurCA 454 PE + Illumina 2x250 PE Assembly Issue

[David_Cleary]

I'm having some issues using MaSurCA to perform a hybrid assembly using 454 PE and Illumina 2x250 PE data for a ~2Mbp bacterial genome. Have converted the .sff to .frg with the necessary linkers using sffToCA. Number of contigs from the hybrid assembly is 900 whereas it is 75 if I only use the illumina data.
Have run out of ideas - any suggestions (except for ditch the 454 data) would be very welcome!
Thanks
David

[David_Cleary]

Ah

masurca doesn't handle 454 mate pairs does it?!?

[flxlex]

It probably doesn't. Split the 454 paired reads using sfftools from Roche, or sff_extract (see methods section of https://flxlexblog.wordpress.com/201...substr-mg1655/)

[David_Cleary]

It probably doesn't. Split the 454 paired reads using sfftools from Roche, or sff_extract (see methods section of https://flxlexblog.wordpress.com/201...substr-mg1655/)

Yeah I tried that but you end up with huge contig numbers owing to the short (pseudo-shotgun) 454 reads. Couldnt find a way to keep the mate pair info so have switched assembler to MIRA. If anyone knows how to do it in MaSuRCA I'd be keen to know though.

Thanks very much though