Published August 30, 2023 | Version 1.0.uniq
Dataset Open

16S V4-V5 metabarcoding reference databases and weighted naive-bayes classifiers, dereplicated

Creators

  • 1. Northern Gulf Institute and NOAA AOML

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

Stats

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
 

 

Notes

"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."

Files

Silva 16S V4-V5 with weights, dereplicated.md

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Additional details

References

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  • Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucl. Acids Res. 42:D643-D648
  • Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Caporaso JG. 2018. Optimizing taxonomic classification of marker gene sequences. Microbiome 6(1): 90. doi: https://doi.org/10.1186/s40168-018-0470-z.
  • Kaehler BD, Bokulich NA, McDonald D, Knight R, Caporaso JG, Huttley GA. 2019. Species-level microbial sequence classification is improved by source-environment information. Nature Communications 10: 4643. https://doi.org/10.1038/s41467-019-12669-6
  • Robeson MS 2nd, O'Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA. RESCRIPt: Reproducible sequence taxonomy reference database management. PLoS Comput Biol. 2021 Nov 8;17(11):e1009581. doi: 10.1371/journal.pcbi.1009581
  • Gonzalez, A. et al. Qiita: rapid, web-enabled microbiome meta-analysis. Nat. methods 15, 796–798 (2018).