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treangenlab / emu

MIT License
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Secondary alignments for short reads #6

Closed TheDBStern closed 5 days ago

TheDBStern commented 3 months ago

Hello,

Great tool! I just wanted to bring to your attention something I learned recently: minimap2 does not report secondary alignments for short reads by default when using the -x sr preset, unless you set --secondary=yes. See https://github.com/lh3/minimap2/issues/846. I know Emu is designed primarily for long reads, but presumably this would impact the short read option.

-David

kdc10 commented 5 days ago

Thanks for bringing this to our attention! Since -N is set to a value greater than 1 (default 50), the --secondary flag should inherently be set to true. Please let us know if you are seeing otherwise in your results.