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Using the SILVA 16S rRNA Database with MetaScope

Aubrey Odom

2024-01-01

Source: vignettes/docs/SILVA.Rmd
SILVA.Rmd

The SILVA database

MetaScope is compatible with the SILVA 16S rRNA Database. At the time of writing, the most recent update to SILVA is version 138.1 (released on August 27, 2020).

Important If you want to use the convert_animalcules_silva() step, you’ll need to use the premade Bowtie2 indices of SILVA 138.1 available here.

You can follow the align_target_bowtie usage outlined in the MetaScope tutorial, replacing the libs parameter with the SILVA indices.

When you reach the metascope_id() step, you will need to include the parameter db = "silva" in the function call to identify down to the genus level using the SILVA taxonomy identifiers.

All CSV outputs from metascope_id() can be compiled into a single MultiAssayExperiment object with the convert_animalcules_silva() function as shown here with false filenames:

out_res <- convert_animalcules_silva(
  meta_counts = all_files,
  annot_path = "animalcules_metadata.csv",
  which_annot_col = "Filename",
  end_string = ".metascope_id.csv",
  qiime_biom_out = FALSE,
  path_to_write = "."
)

saveRDS(out_res, "silva_consolidated_results.RDS")