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martinghunt edited this page May 3, 2016
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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.
Please see the readme from the ARIBA github repository for installation instructions.
The installation installs a single script called ariba, which can be used to run several tasks.
A FASTA file of reference genes is required. This can be sanity checked using
ariba refcheck genes.fasta
and a new, fixed version can be made with
ariba refcheck -o genes.fixed genes.fa
To see all the options, run
ariba refcheck --help