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liaoherui / VirStrain

An RNA virus strain-level identification tool for short reads.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02609-x
MIT License
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Virstrain build sites cutoff default value. #18

Open MTDouglas opened 3 months ago

MTDouglas commented 3 months ago

Hello,

I'm just curious as to what the default value being used in Virstrain_build --sites_cutoff is when no value is specified?

Thanks

liaoherui commented 3 months ago

Hi, thanks for using VirStrain!

By default, VirStrain applies "greedy covering algorithm" to find the minimum sites that can distinguish different viral strains automatically (more details can be found in the manuscript). So, this parameter is not used. This parameter may be needed/added when the sequencing depth or quality is low and we want more sites be covered for strain identification.