ariba-aln2meta(1) Make metadata input to preparef, using multialignment and SNPs

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.