I have a couple yeast assemblies produced with canu with generally nice contiguity, one contig per chromosome. However, for some assembled chromosomes end up splitted into two contigs. Long read coverage clearly indicates that matching ends are composed of duplicated sequences (up to 50 kbp) but ragout scaffolding do not resolved the duplication and concatenate them with Ns.
Does Ragout generally trims contigs ends when scaffolding indicate duplication? Is there a maximum duplicated length that it can handle? Any pointers are welcome.
Ragout in general does not change contig sequences. It may split a contig into parts if it thinks it's chimeric, but it was not designed to trim duplications.
Hello @fenderglass and team,
Thanks for developping this nice tool.
I have a couple yeast assemblies produced with
canu
with generally nice contiguity, one contig per chromosome. However, for some assembled chromosomes end up splitted into two contigs. Long read coverage clearly indicates that matching ends are composed of duplicated sequences (up to 50 kbp) butragout
scaffolding do not resolved the duplication and concatenate them with Ns.Does Ragout generally trims contigs ends when scaffolding indicate duplication? Is there a maximum duplicated length that it can handle? Any pointers are welcome.
Best,
Alan