SYNOPSISariba ,reportfilter /[,options/] ,<infile> <outprefix>/
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
Filters an ARIBA report tsv file
- Name of input tsv file
- Prefix of output files. outprefix.tsv and outprefix.xls will be made
- -h, --help
- show this help message and exit
- --exclude_flags EXCLUDE_FLAGS
- Comma-separated list of flags to exclude. [assembly_fail,ref_seq_choose_fail]
- --min_pc_id FLOAT
- Minimum percent identity of nucmer match between contig and reference [90.0]
- --min_ref_base_asm INT
- Minimum number of reference bases matching assembly 
- Keep synonymous variants (by default they are removed
- Applies to variant only genes. Filter out where there is a known variant, but the assembly has the wild type. By default these rows are kept.
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.