makeSpeciesFasta_RDP: This function creates the dada2 assignSpecies fasta file for...

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

This function creates the dada2 assignSpecies fasta file for the RDP from the RDP's _Bacteria_unaligned.fa file.

Description

THE WAY RDP RELEASES SPECIES LEVEL INFORMATION APPEARS TO HAVE CHANGED IN RELEASE 19 AS A RESULT, THIS OUTPUT IS NOT CURRENTLY BEING MAINTAINED

Usage

makeSpeciesFasta_RDP(fin, fout, compress = TRUE)

Details

## RDP Trainset 18/Release 11.5 ## The RDP documentation does not make clear whether the updates to the taxonomy from training set release 18 were ## propagated to the current Bacterial alignment. dada2:::makeSpeciesFasta_RDP("~/Desktop/RDP/current_Bacteria_unaligned.fa", "~/tax/rdp_species_assignment_18.fa.gz") dada2:::tax.check("~/tax/rdp_species_assignment_18.fa.gz", mode="species")

## RDP Trainset 16/Release 11.5 dada2:::makeSpeciesFasta_RDP("~/Desktop/RDP/current_Bacteria_unaligned.fa", "~/tax/rdp_species_assignment_16.fa.gz")

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