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bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
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Using PopPunk for plasmids #200

Closed andreaniml closed 2 years ago

andreaniml commented 2 years ago

Hello!

I'm wondering if PopPUNK could be aplied to a group of plasmids sequences (some are complete, others are predicted by other software). I believe the program would work, but I don't know if I wouldn't be breaking some statistical assumptions it uses. Can I use popPUNK for clustering plasmids? Cheers!

Maria Luiza

nickjcroucher commented 2 years ago

It's fine in principle, but it will only work when there are at least some shared k-mers between the plasmids - if you use a closely-related set of elements, with a short k-mer size range, then it should work - let us know!