Provided by: ariba_2.12.1+ds-2_amd64
ariba - Antibiotic Resistance Identification By Assembly
ariba <subtool> [options]
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.
Please report bugs to the ARIBA issue tracker: https://github.com/sanger-pathogens/ariba/issues ARIBA(1)