makeTaxonomyFasta_SilvaNR: This function creates the dada2 assignTaxonomy training fasta...

In benjjneb/dada2: Accurate, high-resolution sample inference from amplicon sequencing data

This function creates the dada2 assignTaxonomy training fasta for the official Silva NR99 release files. If 'include.species'=TRUE, a 7th taxonomic level (species) will be added based on the Genus species binomial in the Silva taxonomy string (if consistent with the genus assignment).

Description

## Silva release v138.2 path <- "~/tax/Silva/v138_2" dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"), file.path(path, "tax_slv_ssu_138.2.txt"), "~/Desktop/silva_nr99_v138.2_toGenus_trainset.fa.gz") dada2:::tax.check("~/Desktop/silva_nr99_v138.2_toGenus_trainset.fa.gz")

dada2:::makeTaxonomyFasta_SilvaNR(file.path(path, "SILVA_138.2_SSURef_NR99_tax_silva.fasta.gz"), file.path(path, "tax_slv_ssu_138.2.txt"), include.species=TRUE, "~/silva_nr99_v138.2_toSpecies_trainset.fa.gz") dada2:::tax.check("~/Desktop/silva_nr99_v138.2_toSpecies_trainset.fa.gz")

Usage

makeTaxonomyFasta_SilvaNR(
  fin,
  ftax,
  fout,
  include.species = FALSE,
  compress = TRUE
)

benjjneb/dada2 documentation built on Jan. 12, 2025, 10:03 a.m.