SYNOPSIS

ariba <task> [options]

DESCRIPTION

ariba is the main executable for the ARIBA software. The actual functionality is provided by the subtools:

getref

download reference data

prepareref

prepare reference data for running the pipeline

run

run the ARIBA local assembly pipeline

reportfilter

Filter report.tsv file

summary

summarise multiple reports made by "run"

flag

translate the meaning of a flag output by the pipeline

aln2meta

make metadata input to preparef, using multialignment and SNPs

test

run on small test dataset

version

print version and exit