Silva SSU 138: Prokaryotic 16S rRNA Reference Database for DADA2

Silva Project's version 138 release provides a curated small subunit ribosomal RNA (SSU rRNA) sequence database. These files are specifically formatted as training data for the DADA2 bioinformatics pipeline to classify prokaryotic 16S sequencing data, with an updated method that includes species-level assignments for longer amplicons. The dataset is derived from the Silva database and is intended for bacterial and archaeal analysis, containing only 100 eukaryotic sequences as an outgroup.

Use Cases

• Taxonomic classification of bacterial and archaeal 16S rRNA sequences using the DADA2 `assignTaxonomy` function.
• Benchmarking classification algorithms against a curated, versioned reference database (Silva 138).
• Analyzing long-read amplicon sequencing data where species-level resolution is required.

Strengths

• Derived from the authoritative, versioned Silva Project database (release 138).
• Version 2 includes a greater number of bacterial and archaeal sequences by removing dependence on mothur preprocessing.
• Provides species-level taxonomic assignments suitable for longer amplicons.

Limitations

• Contains known taxonomic problems affecting 10 out of 883 families and 114 out of 3838 genera.
• Not appropriate for classifying eukaryotic Amplicon Sequence Variants (ASVs).
• Key metadata such as row count, file size, and specific update dates are not provided across sources.

Provenance

Source

Silva Project (version 138 release), processed and formatted by Michael R. McLaren.

Collection Method

Fasta files were generated and checked for consistency with version 132 using R code documented in 'silva-v138.Rmd'.