agios: agios

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

Description

Calculates AGIOS (Average Genome Identity of Orthologous Sequences) values for all genomes present in the folder.

Usage

agios(pattern = ".ffn", reference = "all", path = ".",
  outdir = "agios_output", proc = 2)

Arguments

pattern	a pattern (like '.ffn') for recognizing the genome annotation files in nucleotides.
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 genome annotations 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

agios(path='./prodigal_output',pattern='.ffn',reference='all',outdir='agios_result',proc=2)

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