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Disclaimer

This is pre-publication software that is currently under active development. Use it at your own risk. Bug reports are welcome, but user support is not provided at this time.

ARIBA: Antibiotic Resistance Identification By Assembly

ARIBA is a tool that identifies anitbiotic resistance genes by running local assemblies.

The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes.

Installation

Please see the readme from the ARIBA github repository for installation instructions.

Synopsis

Get reference data (in this example, from CARD, but we also support argannot, resfinder, and VFDB, or you can provide your own).

ariba getref card out.card

Prepare reference data for ARIBA

ariba prepareref --ref_prefix out.card out.card.prepareref

Run local assemblies and call variants

ariba run out.card.prepareref reads1.fastq reads2.fastq out.run

Summarise data from several runs (in this case 3)

ariba summary out.summary out.run1/report1.tsv out.run2/report2.tsv out.run3/report3.tsv

View the results in Phandango by dragging and dropping the files out.summary.phnadango.tre and out.summary.phandango.csv into the Phandago window.

Tasks

The installation installs a single script called ariba, which can be used to run several tasks. Run ariba with no options to list all the available tasks. The tasks are:

• 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 a small test dataset
• version: Print versions and exit