The SNVPhyl (SNV PHYLogenomics) pipeline is a pipeline for identifying Single Nucleotide Variants (SNV) within a collection of microbial genomes and constructing a phylogenetic tree. Detailed documentation can be found at http://snvphyl.readthedocs.io/. This repository contains the customized Galaxy tools for this pipeline as well as the source for the documentation.
A command-line interface for SNVPhyl is available at https://github.com/phac-nml/snvphyl-galaxy-cli. This can be used to automatically prepare data and run SNVPhyl in a pre-existing Galaxy instance, or in a custom Docker container. To quickly try out SNVPhyl, the following can be run (assuming Python and Docker are installed).
git clone https://github.com/phac-nml/snvphyl-galaxy-cli.git
cd snvphyl-galaxy && pip install -r requirements.txt
# append `--with-docker-sudo` if docker command requires sudo
python bin/snvphyl.py --deploy-docker --fastq-dir example-data/fastqs --reference-file example-data/reference.fasta --min-coverage 5 --output-dir output1Please see https://github.com/phac-nml/snvphyl-galaxy-cli for more details.
A version of SNVPhyl available for execution in Nextflow has been developed by Jill Hagey and is available at https://github.com/DHQP/SNVPhyl_Nextflow.
The SNVPhyl pipeline is available via a Galaxy toolshed at http://irida.corefacility.ca/galaxy-shed. Dependency tools are installable via the suite_snvphyl_x_y_z tool suite. Workflow files are available at docs/workflows/SNVPhyl/.
Please see http://snvphyl.readthedocs.io/en/latest/install/galaxy/ for more details.
A virtual machine containing the SNVPhyl workflow pipeline and Galaxy is available for download at https://sairidapublic.blob.core.windows.net/downloads/snvphyl-galaxy/snvphyl-galaxy-current.zip or, using Vagrant, can be launched like:
git clone https://github.com/phac-nml/snvphyl-galaxy.git
cd snvphyl-galaxy/vagrant
vagrant upGalaxy and SNVPhyl can then be accessed through http://localhost:48888 with username admin@localhost.localdomain and password adminpassword.
Please see http://snvphyl.readthedocs.io/en/latest/install/virtualmachine/ for more details.
A Docker image of SNVPhyl and Galaxy can be launched by running:
docker run -d -p 48888:80 phacnml/snvphyl-galaxy-1.0.1Galaxy and SNVPhyl can then be access through http://localhost:48888 with username admin@galaxy.org and password admin.
Please see http://snvphyl.readthedocs.io/en/latest/install/docker/ for more details, or https://github.com/bgruening/docker-galaxy-stable for details on the underlying Galaxy Docker image.
Petkau A, Mabon P, Sieffert C, Knox N, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz L, Nadon C, Reimer A, Taboada E, Beiko R, Hsiao W, Brinkman F, Graham M, Van Domselaar G. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. 08/06/2017. M Gen 3(6): doi:10.1099/mgen.0.000116.
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