DESCRIPTION

ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies.

More information on the individual subtools can be found on the ARIBA wiki: https://github.com/sanger-pathogens/ariba/wiki

WARNING: gapfiller not found in path. Looked for GapFiller.pl. But it is optional so will be skipped during assembly WARNING: sspace not found in path. Looked for SSPACE_Basic_v2.0.pl. But it is optional so will be skipped during assembly ARIBA version: 1.0.1

External dependencies: bcftools 1.3.1 ,/usr/bin/bcftools/ bowtie2 2.2.9 ,/usr/bin/bowtie2/ cdhit 4.6 ,/usr/bin/cdhit-est/ gapfiller NA NOT_FOUND nucmer 3.1 ,/usr/bin/nucmer/ r 3.3.1 ,/usr/bin/Rscript/ samtools 1.3.1 ,/usr/bin/samtools/ spades .8.1 ,/usr/bin/spades.py/ sspace NA NOT_FOUND

External dependencies OK: True

Python version: 3.5.2 (default, Jun 27 2016, 06:22:49) [GCC 5.4.0 20160609]

Python packages: ariba 1.0.1 ,/build/ariba-1.0.1/ariba/__init__.py/ openpyxl 2.3.0 ,/usr/lib/python3/dist-packages/openpyxl/__init__.py/ pyfastaq 3.12.1 ,/usr/lib/python3/dist-packages/pyfastaq/__init__.py/ pymummer 0.7.1 ,/usr/lib/python3/dist-packages/pymummer/__init__.py/ pysam 0.9.1 ,/usr/lib/python3/dist-packages/pysam/__init__.py/

Python packages OK: True

Everything looks OK: True

COPYRIGHT

This tool is developed and maintained by the Pathogen Informatics group at the Wellcome Trust Sanger Institute under the GNU General Public License, version 3.