ariba-run(1) Run the ARIBA local assembly pipeline


ariba ,run /[,options/] ,<prepareref_dir> <reads1.fq> <reads2.fq> <outdir>/


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:

positional arguments:

Name of output directory when "ariba prepareref" was run
Name of fwd reads fastq file
Name of rev reads fastq file
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]
Do not clean up intermediate files
--tmp_dir TMP_DIR
Existing directory in which to create a temporary directory used for local assemblies
Be verbose


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.