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These DADA2-formatted training fasta files were derived from the Silva Project's version 138 release. See https://www.arb-silva.de/documentation/release-138/ for database and citation information. The Silva 138 database is licensed under Creative Commons Attribution 4.0 (CC-BY 4.0); see file "SILVA_LICENSE.txt". The fasta files were generated and checked for consistency with version 132 using the R code in the R-markdown document "silva-v138.Rmd". Version 2 removes the dependence on preprocessed files from mothur, which results in a greater number of bacterial and archeal sequences. It also includes a new version of the assignTaxonomy training set that goes through the species level for use with longer amplicons obtained from long-read amplicon sequencing. If you use these files, please cite one or both of the Silva references below (or at the above link) and the DADA2 paper (reference below). I also recommend citing or linking to 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. NOTE: These Version 2 files are intended for use in classifying prokaryotic 16S sequencing data and are not appropriate for classifying eukaryotic ASVs. The new method implemented within DADA2 for constructing these files only includes 100 eukaryotic sequences for use as an outgroup. NOTE: These Version 2 files have a known problem in 10/883 families and 114/3838 genera. See https://github.com/mikemc/dada2-reference-databases/blob/main/silva-138/v2/bad-taxa.csv for a list of affected taxa and https://github.com/benjjneb/dada2/issues/1293 for more information.
{"references": ["Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Gl\u00f6ckner 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, Gl\u00f6ckner 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\u2013583. doi:10.1038/nmeth.3869"]}
taxonomy, DADA2, Silva
taxonomy, DADA2, Silva
citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | 32 | |
popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network. | Top 10% | |
influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically). | Average | |
impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network. | Top 10% |
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