mlst: MLST

In iferres/MLSTar: Quick Multi Locus Sequence Typing Analisys

Description

Perform Multi Locus Sequence Typing.

Usage

mlst(
  genome,
  dbs,
  write = "new",
  prefix = "allele",
  dir = ".",
  dnw = paste0(dir, "tmp/"),
  n_threads = 1L,
  outf = tempdir(),
  pid = 90,
  scov = 0.9
)

Arguments

genome	A FASTA file with the genome sequence.
dbs	Subject database files. No subfix needed.
write	character. One of "new" (Default), "all" or "none". The fist one writes only new alleles found (not reported in pubmlst.org), the second writes all alleles found, and "none" do not write any file.
prefix	character A prefix to the fasta files of found sequences (see write). (Default: "allele").
dir	An existing directory where to put the loci fasta files in case they are not provided by the user. Also sequences found will be placed here if write is set to ethier "new" or "all".
dnw	Temporary directory where to put new alleles to check later if are the same.
n_threads	integer. The number of threads to use by BLASTN.
outf	Where the blastn output will be written.
pid	Percentage identity.
scov	Query coverage.

Value

A vector with the mlst.

Author(s)

Ignacio Ferres

References

Altschul, Gish, Miller, Myers & Lipman. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

Jolley KA, Bray JE, Maiden MCJ. A RESTful application programming interface for the PubMLST molecular typing and genome databases. Database: The Journal of Biological Databases and Curation. 2017;2017:bax060. doi:10.1093/database/bax060.

iferres/MLSTar documentation built on Dec. 30, 2020, 2:42 p.m.