SYNOPSIS
ariba ,summary /[,options/] ,<outprefix> /[,report1.tsv report2.tsv /...]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
Make a summary of ARIBA report files, and Phandango files
positional arguments:
- outprefix
- Prefix of output files
- infiles
- Files to be summarised
optional arguments:
- -h, --help
- show this help message and exit
- -f FILENAME, --fofn FILENAME
- File of filenames of ariba reports in tsv format (not xls) to be summarised. Must be used if no input files listed after the outfile.
- --preset minimal|cluster_small|cluster_all|cluster_var_groups|cluster_known_vars|all|all_no_filter
- Shorthand for setting --cluster_cols,--col_filter,-- row_filter,--known_vars,--novel_vars. Using this overrides those options
- --cluster_cols col1,col2,...
- Comma separated list of cluster columns to include. Choose from: assembled, has_res, ref_seq, pct_id, known_var, novel_var [has_res]
- --col_filter y|n
- Choose whether columns where all values are "no" or "NA" are removed [y]
- --row_filter y|n
- Choose whether rows where all values are "no" or "NA" are removed [y]
- --var_cols col1,col2,...
- Comma separated list of variant columns to include. Choose from: groups, grouped, ungrouped, novel [none by default]
- --min_id FLOAT
- Minimum percent identity cutoff to count as assembled [90]
- --verbose
- Be verbose
Files must be listed after the output file and/or the option --fofn must be used. If both used, all files in the filename specified by --fofn AND the files listed after the output file will be used as input.
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.