ariba - Antibiotic Resistance Identification By Assembly
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.
download reference data
prepare reference data for input to
run the ARIBA local assembly pipeline
get cluster or sequence info from prepareref
Filter report.tsv file
summarise multiple reports made by
translate the meaning of a flag
converts multi-aln fasta and SNPs to
run small built-in test dataset
get versions and exit
You can run
to show more information about how to run each subtool.
Please report bugs to the ARIBA issue tracker:
⟨URL: https://github.com/sanger-pathogens/ariba/issues ⟩