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ARIBA(1)   ARIBA(1)

NAME

ariba - Antibiotic Resistance Identification By Assembly

SYNOPSIS

ariba <subtool> [options]

DESCRIPTION

ariba is the main executable for the ARIBA software, a tool that identifies antibiotic resistance genes by running local assemblies.

In general, the input is a FASTA file of reference sequences (can be a mix of genes and noncoding sequences) and paired sequencing reads. ARIBA reports which of the reference sequence were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference sequences.

The actual functionality is provided by the subtools listed below.

Subtools

getref
download reference data

prepareref

prepare reference data for input to "run"

run

run the ARIBA local assembly pipeline

refquery

get cluster or sequence info from prepareref output

reportfilter

Filter report.tsv file

summary

summarise multiple reports made by "run"

flag

translate the meaning of a flag

aln2meta

converts multi-aln fasta and SNPs to metadata

test

run small built-in test dataset

version

get versions and exit

Subtool help

You can run 

ariba <subtool> --help

to show more information about how to run each subtool.

BUGS

Please report bugs to the ARIBA issue tracker: <https://github.com/sanger-pathogens/ariba/issues>