read.ANI: Read pairwise output from fastANI

In lmc297/bactaxR: Bacterial taxonomy construction and evaluation in R

Read pairwise output from fastANI

Description

This function reads a file of pairwise ANI values calculated by fastANI (or a file of pairwise ANI values constructed using other methods; see below). This file must contain pairwise comparisons for all query and reference genomes (i.e., all-vs-all comparisons).

Usage

read.ANI(file)

Arguments

file

Path to file containing pairwise ANI comparisons output by fastANI (or any 3+ column file, described as follows). The file should not have a header, and should contain 3 or more columns, each separated by a tab. Columns 1, 2, and 3 should contain the query genome, reference genome, and the associated ANI value (ranging from 0 to 100), respectively (remaining columns will be ignored).

Value

A bactaxRObject object

lmc297/bactaxR documentation built on Feb. 6, 2024, 7:41 p.m.