File: ariba.1.adoc

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= 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