search

mapleforest / HaploMerger2

40 stars 6 forks source link

minOverlap and new scaffold connection #3

Open danshu opened 7 years ago

danshu commented 7 years ago

Hi,

It is mentioned in the manual that "HaploMerger is able to connect two scaffolds into one if they share an overlapping region (alignments). The option minOverlap controls the minimum alignment length (excluding Ns, gaps and indels) that can trigger a connecting operation." So repeats will also contribute to the alignment that connects two scaffolds? I noticed that the N50 of setting minOverlap=0 is about twice of that setting minOverlap=999999999. However, I'm not confident about these new connections because the genome is repeat-rich. Can Haplomerger also filter those alignmnet due to repeats?

Best, Danshu

mapleforest commented 7 years ago

Repeats will not become a significant problem here as long as you have soft-masked the genome assembly properly. Soft-masking is the anti-repeat method here.

danshu commented 7 years ago

Thanks!