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:

prepareref_dir

Name of output directory when "ariba prepareref" was run

reads_1

Name of fwd reads fastq file

reads_2

Name of rev reads fastq file

outdir

Output directory (must not already exist)

optional arguments:

-h, --help

show this help message and exit

nucmer options:

--nucmer_min_id INT

Minimum alignment identity (delta-filter -i) [90]

--nucmer_min_len INT

Minimum alignment length (delta-filter -i) [20]

--nucmer_breaklen INT

Value to use for -breaklen when running nucmer [200]

Assembly options:

--assembly_cov INT

Target read coverage when sampling reads for assembly [50]

--assembler_k INT

kmer size to use with assembler. You can use 0 to set kmer to 2/3 of the read length. Warning - lower kmers are usually better. [21]

--spades_other OPTIONS

Put options string to be used with spades in quotes. This will NOT be sanity checked. Do not use -k (see --assembler_k), or -t (use ariba option --threads) [--only-assembler -m 4]

--min_scaff_depth INT

Minimum number of read pairs needed as evidence for scaffold link between two contigs. This is also the value used for sspace -k when scaffolding [10]

Other options:

--threads INT

Number of threads [1]

--bowtie2_preset very-fast-local|fast-local|sensitive-local|very-sensitive-local

Preset option for bowtie2 mapping [very-sensitivelocal]

--assembled_threshold FLOAT (between 0 and 1)

If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [0.95]

--gene_nt_extend INT

Max number of nucleotides to extend ends of gene matches to look for start/stop codons [30]

--unique_threshold FLOAT (between 0 and 1)

If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [0.03]

--noclean

Do not clean up intermediate files

--tmp_dir TMP_DIR

Existing directory in which to create a temporary directory used for local assemblies

--verbose

Be verbose

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.