Introduction

A genomic signature is a genomic locus that is sufficiently represented in an inclusion group, and sufficiently absent from a background, or exclusion group. A signature might correlate genomic features with phenotypic traits, such as the presence of a gene with increased organism pathogenicity.

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. Neptune may be leveraged to reveal discriminatory signature sequences to uniquely delineate one group of organisms, such as isolates associated with a disease cluster or event, from unrelated sporadic or environmental microbes.

Resources

Website: https://phac-nml.github.io/neptune/
Installation: https://phac-nml.github.io/neptune/install/
Walkthrough: https://phac-nml.github.io/neptune/walkthrough/

Release

Neptune 1.2.5

This release provides fixes for ambiguous crashes as a consequence of inputs containing no A, C, G, or T characters, and also makes improvements to the code quality.

Installation

It is strongly recommended you refer to the documentation for full installation instructions. Neptune may be installed on any 64-bit Linux system using Bioconda:

Install Bioconda
Install the "neptune" Bioconda package (conda install neptune).

Neptune may also be installed directly and instructions are available in the documentation.

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 documentation for more details.

Contact

Eric Marinier: eric.marinier@phac-aspc.gc.ca

Legal

Neptune

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.