I am trying to assemble a genome full of repetitive sequences. So far I tested SOAPdenovo2, platanus, (dip)SPAdes and velvet. I noticed a huge difference in the resulting contigs, not only in statistics (N50, number of contigs, etc..), but also on sequence level.
Some contigs seemed to be consistent though all assemblies though, meaning they are probably easiest to assemble and showing good coverage in the data. Is there a tool that uses the output of multiple de Bruijn Graph assemblies to identify trusted contigs that were constructed in all (or most) of the assemblies? Could using mutiple assemblers at the same time be an approach to increase the quality of genome draft?
Thank you in advance!