No description, website, or topics provided.
Switch branches/tags
Nothing to show
Clone or download
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
inputFiles addition of inputfiles Aug 16, 2017
BBMap_37.36.tar.gz working DockerFile Jul 27, 2017
Dockerfile cleaned up dockerfile Aug 22, 2017
LICENSE license MIT Aug 29, 2017
README.md minor readme clarification update Nov 26, 2018
SPAdes-3.10.1-Linux.tar.gz working DockerFile Jul 27, 2017
commands.txt Update commands.txt Aug 18, 2017
g3-iterated-viral.csh major changes Aug 16, 2017
virMine.py major changes Aug 16, 2017
virmine_make_dbs.py update to make databases script Nov 26, 2018

README.md

virMine

Novel viral species genomes – particularly those in high abundance – have been able to be identified directly from complex community viral metagenomes. Discovery of such viral genomes often relies heavily on manual curation and prior studies have employed a variety of different criteria when sifting through sequencing data. In an effort to provide a comprehensive means for the discovery of complete viral genomes from complex sequence data sets, we developed the tool virMine. Raw sequencing reads are processed and assembled and annotated, and individual contigs are scored based upon their likelihood of being viral in origin. Several filters have been implemented, allowing researchers to refine their search for their specific study system. virMine can be used to identify viruses in any niche and thus further our understanding of this vast reservoir of genetic diversity.

Getting Started

Clone Project

git clone https://github.com/thatzopoulos/virmine.git

Move paired-end fastq files, as well as the viral and nonviral databases, to the inputFiles folder prior to building the docker image

From within the project folder run:

sudo docker build -t virmine .
sudo docker run -v /pathToLocalFolder/runName:/virmineDockerOutputFolder -i -t virmine

Prerequisites

Docker is the only prerequisite for this program to run, all other dependencies are handled by the Dockerfile.

virMine Command Options

  • a : choose your assembler (spades, metaspades, megahit, all3)
  • p : list your paired-end read files
  • v : list your viral database
  • nv : list your nonviral database
  • o : make an output file

Example Run

python2.7 virMine.py -a spades -p inputFiles/R1.fastq inputFiles/R2.fastq -v inputFiles/viral_aa.fasta -nv inputFiles/nonviral_aa.fasta -o outputFolder

Authors

  • Andrea Garretto
  • Thomas Hatzopoulos
  • Catherine Putonti

License

This project is licensed under the terms of the MIT License