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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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Does Ragout trim contigs' ends? #87

Closed touala closed 10 months ago

touala commented 10 months ago

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) 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.

Best,

Alan

mikolmogorov commented 10 months ago

Hi Alan,

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.

touala commented 10 months ago

Thanks for the quick answer. Best.