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

positional arguments:

outdir

Output directory (must not already exist)

optional arguments:

-h, --help

show this help message and exit

input files options:

--ref_prefix FILENAME_PREFIX

Prefix of input files (same as was used with getref), to save listing --preseabs,--varonly ...etc. Will look for files called "ref_prefix." followed by: metadata.t sv,presence_absence.fa,noncoding.fa,variants_only.fa. Using this will cause these to be ignored if used: --presabs,--varonly,--noncoding,--metadata

--presabs FILENAME

FASTA file of presence absence genes

--varonly FILENAME

FASTA file of variants only genes

--noncoding FILENAME

FASTA file of noncoding sequences

--metadata FILENAME

tsv file of metadata about the reference sequences

cd-hit options:

--no_cdhit

Do not run cd-hit. Each input sequence is put into its own "cluster". Incompatible with --cdhit_clusters.

--cdhit_clusters FILENAME

File specifying how the sequences should be clustered. Will be used instead of running cdhit. Format is one cluster per line. Sequence names separated by whitespace. First name in line is the cluster representative. Incompatible with --no_cdhit

--cdhit_min_id FLOAT

Sequence identity threshold (cd-hit option -c) [0.9]

--cdhit_min_length FLOAT

length difference cutoff (cd-hit option -s) [0.9]

other options:

--min_gene_length INT

Minimum allowed length in nucleotides of reference genes [6]

--max_gene_length INT

Maximum allowed length in nucleotides of reference genes [10000]

--genetic_code INT

Number of genetic code to use. Currently supported 1,4,11 [11]

--threads INT

Number of threads (currently only applies to cdhit) [1]

--verbose

Be verbose

REQUIRED: either --ref_prefix, or at least one of --presabs, --varonly, --noncoding

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.