anib: anib

In giraola/taxxo: Integrating and automatising tools for prokaryotes taxonogenomics

Description

Calculates ANIb (Average Nucleotide Identity using Blast) values for all genomes present in a directory.

Usage

anib(pattern = ".fna", reference = "all", path = ".",
  outdir = "anib_output", proc = 2)

Arguments

pattern	a pattern (like '.fna') for recognizing the genome files.
reference	is a genome name used to compare one vs. the rest. If set to 'all' (default), all vs. all is computed.
path	is the full path to where genomes assemblies in fasta format are placed.
outdir	a name for the output directory that will be created for results.
proc	is the number of threads for parallel computing.

Examples

anib(path='.',pattern='.fna',reference='all',outdir='anib_result',proc=2)

giraola/taxxo documentation built on May 17, 2019, 5:25 a.m.