Different polisher

[PSchneeb]

Bonjour Jean-Sebastien,

I was wondering if there is any way to "resume" the pipeline at a specified step or if there is a way to analyze/cluster the contigs that were polished using a different polisher (pilon just takes way too long)?

I'm trying to assemble a metagenome using 200M Illumina PE reads and 90M Nanopore reads (Q20+)

Thanks a lot!
Pierre

[jsgounot]

Bonjour Pierre!

OPERA-MS should be able to resume wherever it stopped automatically. So far only Pilon has been implemented and there is no plan to add more polished. The easiest would be to skip the polishing step in OMS (--no-polishing) and to polish (or not) your contigs separately.

Regards,
JS