Hi folks. I need to run a de novo short-read genome assembler (on a paired-end/mate-pair library) that prefers outputting shorter but error-free contigs rather than longer contigs/scaffolds which may be mis-assembled. What assembler or what specific setting in an assembler of choice do you recommend to yield such contigs (as error-free as possible and no contig overlappings)?
According to the first GAGE paper, SGA makes shorter, but very much correct contigs. See http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111.full.pdf