During subsampling, among identical sequences, is there a way or a parameter we can set to always keep the sample with earliest collection date? Or is it something we should do before feeding data to Nextstrain? Thanks!

is there a reason why you do not want to keep identical sequences? It’s quite common for many samples to have identical sequences if a lot of cases are sequenced. augur filter does not check the sequences themselves for identity. So you would have to script something yourself - e.g. hashing sequen…

Thanks. So if every case is sequenced only once, you should not exclude identical sequences - or does the method not work if you have multiple identical sequences?

It’s Bayesian analysis - cannot handle all that much data XD

Is there a way to keep the oldest sample among identical sequences?

Help and Getting Started

dlu June 30, 2022, 4:19pm 3

We’re trying to do representative subsampling for phylodynamics analysis. Very good to know, thanks!!

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Is there a way to keep the oldest sample among identical sequences?

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