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PacificBiosciences / HiFi-16S-workflow

Nextflow pipeline to analyze PacBio HiFi full-length 16S data
BSD 3-Clause Clear License
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adding the greengenes2 naive bayes classifier #56

Open splaisan opened 1 month ago

splaisan commented 1 month ago

Dear , @proteinosome and @fripp

Would it ber possible to upgrade qiime2 to the latest version (2024.5 as I write) and add greengenes2 (q2-greengenes2 and accompanying classifier database) as an alternative source to classify full length 16S sequences. Greengenes2 relies on full length assemblies and is likely becoming soon a new standard for 16S V1V9 and is being actively developped (https://forum.qiime2.org/t/introducing-greengenes2-2022-10/25291).

Newer versions of the current databases may also be relevant and are linked at https://resources.qiime2.org/

A proper guide on what to change to implement this would already be great value.

Thanks in advance Stephane

proteinosome commented 1 month ago

@splaisan I'll look into this in the next few weeks. Unfortunately I can't promise a solid timeline here, but I'll make sure to get to this as soon as I can.