doi: 110.1099/mgen.0.000131 ariba is maintained by sanger-pathogens. Hunt M, Mather AE, Sánchez-Busó L, Page AJ, Parkhill J, Keane JA, Harris SR. CitationĪRIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
However, the community might be able to help you out if you report any issues about usage of the software to the issues page. We currently do not have the resources to provide support for Ariba. LicenseĪRIBA is free software, licensed under GPLv3. Please read the ARIBA wiki page for full usage instructions. Summary Summarise multiple reports made by "run" Refquery Get cluster or sequence info from prepareref output Get list of available species from PubMLST
Pubmlstget Download species from PubMLST and make db Prepareref Prepare reference data for input to "run" Micplot Make violin/dot plots using MIC data
h, -help show this help message and exitĪln2meta Converts multi-aln fasta and SNPs to metadataĮxpandflag Expands flag column of report file Get reference data, for instance from CARD. ARIBA reports which of the reference sequences were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference sequences. The input is a FASTA file of reference sequences (can be a mix of genes and noncoding sequences) and paired sequencing reads. PLEASE NOTE: we currently do not have the resources to provide support for Ariba - see the Feedback/Issues section.ĪRIBA is a tool that identifies antibiotic resistance genes by running local assemblies. ARIBA Antimicrobial Resistance Identification By Assembly View on GitHub ARIBAĪntimicrobial Resistance Identification By Assemblyįor how to use ARIBA, please see the ARIBA wiki page.
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