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Neptune

Legal

Neptune

Copyright Government of Canada 2015-2017

Written by: Eric Marinier, Public Health Agency of Canada, National Microbiology Laboratory

Funded by the National Micriobiology Laboratory and the Genome Canada / Alberta Innovates Bio Solutions project "Listeria Detection and Surveillance using Next Generation Genomics"

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Description

Neptune locates genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches. The software identifies sequences that are sufficiently represented within inclusion targets and sufficiently absent from exclusion targets. The signature discovery process is accomplished using probabilistic models instead of heuristic strategies.

Release

Neptune 1.2.4

This release makes several small improvements, including: reducing the standard output clutter, adding timings to stages, and updating the documentation.

Requirements

Neptune requires Python 2.7. You may check the installed version with the following:

$ python --version

If running a Debian distribution (ex: Ubuntu), dependencies may be installed using the following command:

$ sudo install/debian_dependencies.sh

Otherwise, the following dependencies must be installed manually:

  • python-pip
  • python-virtualenv
  • build-essential
  • python-dev
  • NCBI BLAST+

Installation

It is strongly recommended you refer to the manual for full installation instructions. Neptune may be installed using the following command:

    $ INSTALL.sh

You may specify an install PREFIX location, and Neptune will install into PREFIX/lib and PREFIX/bin. This only requires security privileges if the install location requires them.

Running Neptune

Neptune's command line arguments can be found by running:

$ neptune --help

A simple example of running Neptune:

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

Please refer to the manual for more details.

Contact

Eric Marinier: [email protected]