SYNOPSIS
ariba ,prepareref /[,options/] ,<outdir>/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.