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friend1ws / nanomonsv

SV detection tool for nanopore sequence reads
GNU General Public License v3.0
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Recomanded settings for Dorado basecaller #50

Closed zhengzhenxian closed 10 months ago

zhengzhenxian commented 10 months ago

Hi, @friend1ws

Thanks for developing this great tool! I've come across a base quality cut-off feature for different settings (--qv10, --qv15, and --qv20). If I'm understanding correctly, does the--qv20 option specifically cater to Q20+ chemistry and the Dorado basecalling?

Additionally, I've noticed that starting from version 0.7.1, there is support for duplex somatic SV calling. Does this feature also utilize the --qv20 option?

Thanks in advance!

Zhenxian

friend1ws commented 10 months ago

Thanks for your interest in nanomonsv. I think --qv20 would be an appropriate choice for Q20+ chemistry (+ Dorado calling), though I believe other settings (such as --qv15 or --qv25) would work to some extent.

Also, --qv20 will not cause any problems for duplex sequence data. So please try!

zhengzhenxian commented 10 months ago

Thanks for your prompt reply!

I will try the option --qv20 option first and will keep updating if I find anything interesting.