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lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
MIT License
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Reads extending over the edge of the contig #75

Closed diego-rt closed 1 year ago

diego-rt commented 1 year ago

Hello,

I was wondering how does racon handle reads that extend over the edge of the contig? Will it extend the contig? Or do you need to have N's at the ends in order to extend them?

Thanks a lot!

Diego

rvaser commented 1 year ago

Hi Diego, I would say it depends on the alignment. If it is a soft clip, the contig won't be extended. If it is somehow an insertion followed by a match/mismatch at the end, it might get extended but depends on how many reads agree on it.

Best regards, Robert