Skip to content

phac-nml/neptune

Folders and files

NameName
Last commit message
Last commit date

Latest commit

48b1ab5 · Feb 27, 2017
Sep 9, 2016
Feb 27, 2017
Feb 27, 2017
Sep 28, 2016
Feb 27, 2017
Feb 23, 2017
Nov 17, 2015
Sep 8, 2016
Feb 27, 2017
Feb 22, 2017
Nov 17, 2015
Feb 27, 2017
Feb 27, 2017
Feb 27, 2017
Sep 9, 2016

Repository files navigation

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]