DOI: 10.5281/zenodo.8302188
title: 16S V4-V5 metabarcoding reference databases and weighted naive-bayes classifiers, dereplicated

description: 16S metabarcoding databases and naive-bayes classifiers specific to the V4-V5 region. Built from the Silva 138.1 SSU Ref NR 99 database using Qiime2 (version 2023.2) and the q2-clawback plugin. Includes weighted classifiers for two Earth Microbiome Project Ontology (EMPO) 3 habitat types: "sediment (saline)" and "water (saline)" , with data downloaded from Qiita. Sequences were dereplicated with Rescript --p-mode 'uniq' , retaining identical sequence records that have differing taxonomies. Primers used: EMP 16S 515f: GTGYCAGCMGCCGCGGTAA EMP 16S 926r: CCGYCAATTYMTTTRAGTTT <strong>Stats</strong> 286,948 unique sequences 309,567 total sequences 46,254 unique taxa (Level 7) File description File Description make new 16S silva V4-V5 database.md Markdown with code used to generate databases silva-138-99-seqs.qza Full length Silva 138.1 SSU 99 sequences silva-138-99-tax.qza Taxa for full length Silva 138.1 SSU 99 database silva-138_1-99-515f_926r-uniq-seqs.qza Sequences for 16S V4-V5 (primers 515f, 926r), extracted from Silva 138.1 SSU 99, generated by qiime2-2023.2 (forward compatible), dereplicated silva-138_1-99-515f_926r-uniq-taxa.qza Taxa for silva-138_1-99-515f_926r-seqs.qza database, dereplicated uniform-silva-138_1-99-515f_926r-uniq-classifier.qza Unweighted (uniform) naive-bayes classifier for 16S V4-V5 (primers 515f, 926r) extracted from Silva 138.1 SSU 99, generated by qiime2-2023.2 (forward compatible) silva-138_1-99-515f_926r-uniq-sediment-saline-classifier.qza Weighted naive-bayes classifier for 16S V4-V5 (primers 515f, 926r) extracted from Silva 138.1 SSU 99, weighted for sediment-saline, generated by qiime2-2023.2 (forward compatible) silva-138_1-99-515f_926r-q2_2023_2-uniq-sediment-saline-weights.qza Weights used to generate silva-138_1-99-515f_926r-q2_2023_2-sediment-saline-classifier.qza silva-138_1-99-515f_926r-uniq-water-saline-classifier.qza Weighted naive-bayes classifier for 16S V4-V5 (primers 515f, 926r) extracted from Silva 138.1 SSU 99, weighted for water-saline, generated by qiime2-2023.2 (forward compatible) silva-138_1-99-515f_926r-uniq-water-saline-weights.qza Weights used to generate silva-138_1-99-515f_926r-water-saline-classifier.qza
description: "This work was supported by award NA21OAR4320190 to the Northern Gulf Institute from NOAA's Office of Oceanic and Atmospheric Research, U.S. Department of Commerce."
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