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

                                                                                         ARIBA(1)