makeTaxonomyFasta_GG2: 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 from the GreenGenes2 release files. If 'include.species'=TRUE, the 7th taxonomic level (species) will be output. Otherwise only the first 6 taxonomic levels (down to genus) will output.

Description

## Greengenes2 release 2024_09 path <- "~/tax/GG2/2024_09" setwd(path) # download.file("http://ftp.microbio.me/greengenes_release/current/2024.09.backbone.full-length.fna.qza", "2024.09.backbone.full-length.fna.qza") download.file("http://ftp.microbio.me/greengenes_release/current/2024.09.backbone.tax.qza", "2024.09.backbone.tax.qza") unzip("2024.09.backbone.full-length.fna.qza") unzip("2024.09.backbone.tax.qza") fn <- "5b42d9b6-2f24-4f01-b989-9b4dafca7d5e/data/dna-sequences.fasta" txfn <- "b7c3e691-ea51-4547-94dd-f79f49e41a36/data/taxonomy.tsv"

Usage

makeTaxonomyFasta_GG2(
  fn,
  txfn,
  fout,
  include.species = FALSE,
  output.binomials = FALSE,
  compress = TRUE
)

Details

fn.out <- "~/Desktop/gg2_2024_09_toGenus_trainset.fa.gz" dada2:::makeTaxonomyFasta_GG2(fn, txfn, fn.out, include.species=FALSE, compress=TRUE) dada2:::tax.check(fn.out)

fn.out.spc <- "~/Desktop/gg2_2024_09_toSpecies_trainset.fa.gz" dada2:::makeTaxonomyFasta_GG2(fn, txfn, fn.out.spc, include.species=TRUE, compress=TRUE) dada2:::tax.check(fn.out.spc)

benjjneb/dada2 documentation built on Dec. 5, 2024, 4:02 p.m.