SYNOPSIS
ariba ,aln2meta /[,options/] ,<aln_fasta> <variants_tsv> <(non)coding> <cluster_rep> <outprefix>/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
Converts multi-alignment fasta and SNP info to metadata
positional arguments:
- aln_fasta
- Multi-fasta file of alignments
- variants_tsv
- TSV file of variants information
- (non)coding
- Sequences are coding or noncoding. Must be one of: coding noncoding
- cluster_rep
- Name of sequence to be used as cluster representative. Must exactly match a sequence in aln_fasta file
- outprefix
- Prefix of output filenames
optional arguments:
- -h, --help
- show this help message and exit
- --genetic_code INT
- Number of genetic code to use. Currently supported 1,4,11 [11]
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.