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This is pre-publication software that is currently under active development. Use it at your own risk. Bug reports are welcome, but user support is not provided at this time.
ARIBA is a tool that identifies anitbiotic resistance genes by running local assemblies.
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 sequences were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference sequences.
Please see the readme from the ARIBA github repository for installation instructions.
Get reference data. In this example, from CARD, but we also support several others (see getref for a full list), or you can provide your own.
ariba getref card out.card
Prepare reference data for ARIBA
ariba prepareref -f out.card.fa -m out.card.tsv out.card.prepareref
Run local assemblies and call variants
ariba run out.card.prepareref reads1.fastq reads2.fastq out.run
Summarise data from several runs (in this case 3)
ariba summary out.summary out.run1/report1.tsv out.run2/report2.tsv out.run3/report3.tsv
View the results in
Phandango
by dragging and dropping the files out.summary.phandango.tre and
out.summary.phandango.csv into the Phandago window.
The installation installs a single script called ariba, which can be used to run
several tasks. Run ariba with no options to list all the available tasks.
The tasks are:
- getref: Download reference data
- prepareref: Prepare reference data for running the pipeline
- refquery: Get cluster or sequence info from prepareref output
- run: Run the ARIBA local assembly pipeline
-
summary: Summarise multiple reports made by
run - flag: Translate the meaning of a flag output by the pipeline
- aln2meta: Make metadata input to preparef, using multialignment and SNPs
- test: Run on a small test dataset
- version: Print versions and exit