multiple passes?

[colindaven]

Hi,

part of the output generated is called -pass1.

Does this imply there might be advantages to iterative scaffolding ? I haven't tried this yet, have you ?

Also, I went up on coverage from the default 3 linking ( uniquely mapped) reads to 10 reads, and while only ~4000 as opposed to ~6500 new scaffolds were created, these appear to be better supported and may contain more contigs in the new scaffolds. I guess the higher number of reads used might lead to less ambiguous or cyclical links between contigs, which are subsequently removed.

Thanks, Colin