ARIBA
=====
Antibiotic Resistance Identification By Assembly
For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
Installation
------------
ARIBA has the following dependencies, which need to be installed:
* [Python3][python] version >= 3.4
* [R][r] version >= 2.14.0
* The R package [ape][ape] version >= 3.1
* [Bowtie2][bowtie2] version >= 2.1.0
* [CD-HIT][cdhit] version >= 4.6
* [Samtools and BCFtools][samtools] version >= 1.2
* [MUMmer][mummer] version >= 3.23
* [SPAdes][spades] version >= 3.5.0
* [Python2][python] version >= 2.7 (SPAdes needs python2)
ARIBA has the following optional dependencies. If they are installed,
they will be used. Otherwise scaffolding and gap filling will be
skipped.
* [SSPACE-basic scaffolder][sspace]
* [GapFiller][gapfiller]
Once the dependencies are installed, install ARIBA using pip:
pip3 install ariba
Alternatively, you can download the latest release from this github repository,
or clone the repository. Then run the tests:
python3 setup.py test
If the tests all pass, install:
python3 setup.py install
### Dependencies and environment variables
By default, ARIBA will look for the dependencies in your `$PATH`, using
the names in the table below. This behaviour can be overridden and
point ARIBA to a specific program using environment variables.
The environment variable is checked first and is used if it is set.
Otherwise ARIBA looks in your `$PATH` for the default name. This applies
to the following dependencies.
| Dependency | Default | Environment variable name |
|----------------|------------------------|---------------------------|
| BCFtools | `bcftools` | `$ARIBA_BCFTOOLS` |
| Bowtie2 | `bowtie2` | `$ARIBA_BOWTIE2` |
| CD-HIT | `cd-hit-est` | `$ARIBA_CDHIT` |
| GapFiller | `GapFiller.pl` | `$ARIBA_GAPFILLER` |
| R | `Rscript` | `$ARIBA_R` |
| Samtools | `samtools` | `$ARIBA_SAMTOOLS` |
| SPAdes | `spades.py` | `$ARIBA_SPADES` |
| SSPACE | `SSPACE_Basic_v2.0.pl` | `$ARIBA_SSPACE` |
For example, you could specify an exact version of Samtools using
(assuming BASH):
export ARIBA_SAMTOOLS=/path/to/samtools
The path need not be absolute. ARIBA looks for the value of the variable
in your $PATH. For example, suppose you have `samtools-0.1.19` and
`samtools-1.3` installed. You could use this:
export ARIBA_SAMTOOLS=samtools-1.3
Usage
-----
Please read the [ARIBA wiki page][ARIBA wiki] for usage instructions.
Build status: [](https://travis-ci.org/sanger-pathogens/ariba)
[bowtie2]: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
[cdhit]: http://weizhongli-lab.org/cd-hit/
[ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki
[gapfiller]: http://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller
[mummer]: http://mummer.sourceforge.net/
[samtools]: http://www.htslib.org/
[spades]: http://bioinf.spbau.ru/spades
[sspace]: http://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE
[ape]: https://cran.r-project.org/web/packages/ape/index.html
[r]: https://www.r-project.org/
[python]: https://www.python.org/