Man pages sections > man1 > ariba

ariba - Antibiotic Resistance Identification By Assembly

ARIBA(1)   ARIBA(1)

NAME

ariba - Antibiotic Resistance Identification By Assembly

SYNOPSIS

ariba <subtool> [options]

DESCRIPTION

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.

BUGS

Please report bugs to the ARIBA issue tracker:
⟨URL: https://github.com/sanger-pathogens/ariba/issues ⟩