getBlastTaxAnnot: getBlastTaxAnnot

Description Usage Arguments Details Value Author(s)

Description

Annotate amplified sequence variants (ASVs) with taxa labels derived from a BLAST search.

Usage

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getBlastTaxAnnot(MA, dataBaseDir = Sys.getenv("BLASTDB"), db = "nt/nt",
  num_threads = 10, negative_gilist = "/SAN/db/blastdb/uncultured.gi",
  infasta = paste0(tempfile(), ".fasta"), outblast = paste0(tempfile(),
  ".blt"), taxonSQL = "/SAN/db/taxonomy/taxonomizr.sql")

Arguments

MA

A MultiAmplicon for which taxa shoudl be annotated. This should contain a sequenceTableNoChime slot, meaning that the MultiAmplicon pipeline needs to be followed to that point.

dataBaseDir

The base directory of your blast databases. This corresponts to, and is by default obtained from the environmental variable $BLASTDB.

db

The blast database. Either a full path or the path relative to the dataBaseDir.

num_threads

The number of threads used for the blast search.

negative_gilist

A file containing NCBI GI numbers to exclude from blast searches.

infasta

A fasta file generated for the blast searche, a temporary file in the respective R temporary folder by default.

outblast

A blast tabular output file generated by the blast searche, a temporary file in the respective R temporary folder by default.

taxonSQL

An SQL file generated by the package taxonomizeR

Details

Based on a BLAST search taxonomic labels are assigned to ASVs. Currently supported taxonomy levels are c("superkingdom", "phylum", "order", "family", "genus", "species"). For each taxonomic level unique best taxa (based on bitscores) are reported. If no unique best taxon exists at a particular level NA is returned for this. The function combines evidence for taxnomic annotations in case of seperate HSPs for (concatenated) non-merged sequences.

Value

An MultiAmplicon object with the taxonomy slot filled

Author(s)

Emanuel Heitlinger


derele/MultiAmplicon documentation built on May 15, 2019, 5:04 a.m.