ariba-summary(1) Summarise multiple reports made by run

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.