SYNOPSIS

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

Filters an ARIBA report tsv file

positional arguments:

infile

Name of input tsv file

outprefix

Prefix of output files. outprefix.tsv and outprefix.xls will be made

optional arguments:

-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 [1]

--keep_syn

Keep synonymous variants (by default they are removed

--discard_without_known_var

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.

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.