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: