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 [this paper][1] in BMC Bioinformatics journal:

 - For short read libraries (e.g. Illumina MiSeq): **CLC bio assembler** ([CLC Assembly Cell][2]) (commerical, free 2-week trial)
 - For Roche 454 read libraries: **Newbler** (Roche)

These assemblers tend to break reads and contigs at repeat boundaries and place repeated elements into separate contigs. Hence we might have more conservative and better quality (less likely to be mis-assembled) contigs.

 [1]: http://www.biomedcentral.com/1471-2105/15/211/abstract
 [2]: http://www.clcbio.com/products/clc-assembly-cell/