Parameters

A help message may be viewed by running:

neptune --help

Mandatory

Neptune requires the location of the inclusion, exclusion, and output directories. The remaining parameters will be estimated based on the input sequence or revert to default settings. The following is the minimum number of command line parameters required to run Neptune:

neptune
    --inclusion /path/to/inclusion/directory/
    --exclusion /path/to/exclusion/directory/
    --output /path/to/output/directory/

The following parameters are required by Neptune:

Option	Alternative	Parameter	Description
-i	--inclusion	FASTA	A list of inclusion targets in FASTA format. You may list multiple file or directory locations following the parameter. Neptune will automatically include all files within directories. However, Neptune will not recurse into additional directories.
-e	--exclusion	FASTA	A list of exclusion targets in FASTA format. You may list multiple file or directory locations following the parameter. Neptune will automatically include all files within directories. However, Neptune will not recurse into additional directories.
-o	--output	directory	The location of the output directory. If this directory exists, any files produced with existing names will be overwritten. If this directory does not exist, then it will be created.

Optional

The optional parameters will either be automatically calculated or be assigned default values.

k-mer

The following parameters relate to k-mer generation and aggregation:

Option	Alternative	Parameter	Description
-k	--kmer	integer	The size of the k-mers. This must be a positive integer and should be large enough such that random intra-genome k-mer matches, within the largest genome, are unexpected. The size of k-mers cannot be larger than the smallest sequence record. This will be automatically calculated if not specified.
	--organization	integer	The degree of organization of k-mer counting and aggregation. This parameter determines the number nucleotide bases used in parallelized k-mer counting and, in turn, the number of parallel instances of k-mer aggregation. The number of parallel instances is determined by 4^n, where n is the specified organization parameter. This value must be a non-negative integer smaller than k. If the parameter is not specified, then n = 0 and there will be no parallel k-mer aggregation. This will likely require a much longer computation time to complete k-mer aggregation.

Filtering

The following command-line parameters relate to signature filtering:

Option	Alternative	Parameter	Description
	--filter-length	float	The minimum percent length of a signature candidate against a exclusion target required to filter out the candidate. This value is a percentage expressed as a floating point number [0.0, 1.0]. If the any exclusion hit exceeds the percent length and percent identity of any candidate, the candidate is removed. The default value is 0.5.
	--filter-percent	float	The minimum percent identity of a signature candidate against a exclusion target required to filter out the candidate. The percent identity is calculated as identities divided by the alignment length. This value is a percentage expressed as a floating point number [0.0, 1.0]. If the any exclusion hit exceeds the percent length and percent identity of any candidate, the candidate is removed. The default value is 0.5.
	--seed-size	integer	The seed size used for alignments. This value must be no smaller than 4. The default value is 11.

Extraction

The following command-line parameters relate to signature extraction:

Option	Alternative	Parameter	Description
-r	--reference	FASTA	A list of references from which to extract signatures. If this parameter is not specified, signatures will be extracted from all inclusion targets. You may list multiple file locations following the --reference parameter.
	--rate	float	The probability (0.0, 1.0) that any two homologous bases are different from each other. This should incorporate mutation rates, sequencing error rates, and assembly error rates. The rate is used to calculate the maximum allowable gap size in a signature and the minimum expected number of exact k-mer matches in a signature. If this value is not specified, the rate is assumed to be 0.01.
	--gc-content	float	The expected GC-content of the environment. The GC-content is used to calculate the maximum allowable gap size in a signature and the minimum expected number of exact k-mer matches in a signature. If this value is not specified, it is calculated by observing the GC-content of each target during signature extraction. The value must be between (0.0, 1.0).
	--confidence	float	The statistical confidence of decision making in the software. The confidence affects the automatic calculation of both the maximum gap size and minimum number of inclusion hits. If this value is not specified, a default of 0.95 is used. The value must be between (0.0, 1.0).
	--inhits	integer	The minimum number of inclusion hits required to start and continue signature extraction. If this value is not specified, it will be automatically calculated using the number of inclusion targets, the GC-content, the rate, and the k-mer size. The calculation can be found in the Mathematics documentation. This value must be a positive integer.
	--exhits	integer	The minimum number of exclusion hits necessary to stop extraction of a signature. If this value is not specified, it is assumed to be 1. This value must be a positive integer.
	--gap	int	The maximum allowable number of base positions shifted before seeing an exact k-mer match. If this value is not specified, it will be automatically calculated using the rate, GC-content, and the k-mer size. The calculation can be found in the Mathematics documentation. This value must be a positive integer.
	--size	int	The minimum size for a signature. Signatures which are shorter than this length will not be reported. If this value is not specified, the minimum signature size will be four times the length of the k-mer size. It is not recommended to locate signatures smaller than this size, unless application-specific. This value must be a positive integer.

Parallelization

The following parameters relate to the parallelization of Neptune:

Option	Alternative	Parameter	Description
-p	--parallelization	integer	The number of parallel working processes to create when Neptune is operating in a non-DRMAA mode (default). This parameter will directly increase the speed of many stages of the software, provided there are sufficient resources available to run the worker process simultaneously. This value must be a positive integer. The default value is 8.

DRMAA

It may be necessary to specify job submission parameters that are required by your cluster-computing environment. If you require DRM-specific command line arguments, they may be provided to Neptune using one of several arguments. The --default-specification parameter will provide the DRM-specific arguments to all jobs which are created. Additional command line arguments allow precise specifications for each type of job.

Option	Alternative	Parameter	Description
	--drmaa	flag	This flag enables DRMAA-based Neptune execution. This will require a DRMAA-compatible cluster computing environment to be installed and configured. However, Neptune will likely operate significantly faster in this environment.
	--default-specification	string	DRMAA-specific command line arguments for all jobs. These arguments must be provided as a quoted string. The default specification will be applied to all job types and overwritten when specified.
	--count-specification	string	DRMAA-specific command line arguments for \textit{k}-mer counting. These arguments must be provided as a quoted string. These arguments will overwrite the default specification, if specified, for this job type.
	--aggregate-specification	string	DRMAA-specific command line arguments for \textit{k}-mer aggregation. These arguments must be provided as a quoted string. These arguments will overwrite the default specification, if specified, for this job type.
	--extract-specification	string	DRMAA-specific command line arguments for signature extraction. These arguments must be provided as a quoted string. These arguments will overwrite the default specification, if specified, for this job type.
	--database-specification	string	DRMAA-specific command line arguments for database construction. These arguments must be provided as a quoted string. These arguments will overwrite the default specification, if specified, for this job type.
	--filter-specification	string	DRMAA-specific command line arguments for candidate signature filtering. These arguments must be provided as a quoted string. These arguments will overwrite the default specification, if specified, for this job type.
	--consolidate-specification	string	DRMAA-specific command line arguments for signature consolidation. These arguments must be provided as a quoted string. These arguments will overwrite the default specification, if specified, for this job type.