Published July 26, 2023
| Version Version 1
Dataset
Open
DADA2 formatted Silva SSU taxonomic training data (Silva version 138.1) with emended description of the genus Lactobacillus Beijerinck 1901
Description
These training fasta files are derived from the Silva 138.1 prokaryotic SSU taxonomic training data formatted for DADA2 (from https://zenodo.org/record/4587955). The species assignment file contains changes in species names according to Zheng et al. 2020 based on data from Lactotax (file 2023_05_30.xlsx). The script in R for making changes in species names is in the silva.R file.
Please cite one or both of the Silva references, the DADA2 paper (reference below), and the Zenodo record for this specific version in your Methods or published source code to record the specific taxonomic database files used in your analysis.
Files
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(230.0 MB)
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Additional details
Related works
- Is derived from
- 10.5281/zenodo.4587955 (DOI)
References
- Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucl. Acids Res. 41 (D1): D590-D596.
- 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.
- Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13:581–583. doi:10.1038/nmeth.3869.