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Taxonomic classification using the Sintax algorithm

Source: R/vs_sintax.R
vs_sintax.Rd

vs_sintax classifies sequences using the Sintax algorithm implemented in VSEARCH.

Usage

vs_sintax(
  fasta_input,
  database,
  outfile = NULL,
  cutoff = 0,
  strand = "plus",
  sintax_random = TRUE,
  randseed = NULL,
  logfile = NULL,
  threads = 1,
  vsearch_options = NULL,
  tmpdir = NULL
)

Arguments

fasta_input

(Required). A FASTA file path or a FASTA object with reads to classify, see Details.

database

(Required). A FASTA file path or a FASTA object containing the reference database in FASTA format. The sequences need to be annotated with taxonomy, see Details.

outfile

(Optional). Name of the output file. If NULL (default), results are returned as a data.frame.

cutoff

(Optional). Minimum level of bootstrap support (0.0-1.0) for the classifications. Defaults to 0.0.

strand

(Optional). Specifies which strand to consider when comparing sequences. Can be either "plus" (default) or "both".

sintax_random

(Optional). If TRUE (default), the Sintax algorithm breaks ties between sequences with equally many kmer matches by a random draw.

randseed

(Optional). Seed for the random number generator used in the Sintax algorithm. Defaults to NULL.

logfile

(Optional). Name of the log file to capture messages from VSEARCH. If NULL (default), no log file is created.

threads

(Optional). Number of computational threads to be used by VSEARCH. Defaults to 1.

vsearch_options

(Optional). A character string of additional arguments to pass to VSEARCH. Defaults to NULL. See Details.

tmpdir

(Optional). Path to the directory where temporary files should be written when tables are used as input or output. Defaults to NULL, which resolves to the session-specific temporary directory (tempdir()).

Value

If outfile is NULL a data.frame is returned. If it contains a file name (text) the data.frame is written to that file with tab-separated columns.

The data.frame contains the classification results for each input sequence. Both the Header and Sequence columns of fasta_input are copied into this table, and in addition are also the columns for each rank. The ranks depend on the database file used, but are typically domain, phylum, class, order,family, genus and species. For each classification is also a bootstrap support score. These are in separate columns with corresponding names, i.e. domain_score, phylum_score, etc.

Details

The sequences in the input file are classified according to the Sintax algorithm, using VSEARCH, see https://www.biorxiv.org/content/10.1101/074161v1.

fasta_input can either be a file path to a FASTA file or a FASTA object. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta.

database can either be a file path to a FASTA file or a FASTA object. FASTA objects are tibbles that contain the columns Header and Sequence, see readFasta. The Header texts of this file must follow the sintax-pattern, see make_sintax_db.

vsearch_options allows users to pass additional command-line arguments to VSEARCH that are not directly supported by this function. Refer to the VSEARCH manual for more details.

References

https://github.com/torognes/vsearch https://www.biorxiv.org/content/10.1101/074161v1

Examples

if (FALSE) { # \dontrun{
# Example files
db.file <- file.path(file.path(path.package("Rsearch"), "extdata"),
                     "sintax_db.fasta")
fasta.file <- file.path(file.path(path.package("Rsearch"), "extdata"),
                     "small.fasta")

tax.tbl <- vs_sintax(fasta_input = fasta.file, database = db.file)
View(tax.tbl)
} # }