Using the SILVA 16S rRNA Database with MetaScope

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). These notes will supplement the main MetaScope pipeline as illustrated in the vignette.

SILVA Indices

Currently, MetaScope is only functional with SILVA when using the premade Bowtie2 indices of SILVA 138.1 available here. In this case,

Accessions

Before running any samples, you’ll need to run download_accessions() with the argument silva_taxonomy_database = TRUE.

Alignment

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

Identification

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.

MetaBLAST

You can use metascope_blast() to refine results from metascope_id().

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")