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SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator

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INTRODUCTION

SVEngine (Structural Variants Engine)

  • SVEngine is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.
  • SVEngine takes as input reference contigs in FASTA files, variant meta distribution as specified in META files (see Manual) or specific variant information as specified in VAR files (see Manual) and NEWICK files for specifying clonal phylogenetic trees in cancer.
  • SVEngine outpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), simulated short read in FASTQ files and aligned short reads in BAM files.
  • SVEngine's modeling and pipeline are illustrated in Figures 1 and 2.

Figure 1. The principle and workflow of SVEngine.

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Figure 2. The bioinformatics pipeline of SVEngine.

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Currently the package works for Linux (tested with Ubuntu) and Mac (tested with Homebrew). It might also work for Windows with Cygwin (not tested). SVEngine documentation is on wiki and it is available: http://bitbucket.org/charade/svengine/wiki

DOCKER (Platform Indepedent)

Due to the multiple R and Python dependencies involved, the easiest way to use SVEngine is by the provided docker image build file. A Dockerfile is provided to build SVEngine-enabled image from a standard Ubuntu docker image. If you are not familiar with Docker, it is a container platform widely used in industry/academia. Here is the link to the Docker community:

docker community .

If you have a docker server running, just need to download the Dockerfile from:

dockerfile

into $your_swan_container and run:

docker build --no-cache $your_swan_container

INSTALL

SVEngine is available on bitbucket: bitbucket.org:charade/svengine.git

Dependencies:

Python2(>=2.7) http://www.python.org/

pybedtools, pysam, pandas, tables, scipy, dendropy, cython

Samtools>=1.2, Bedtools>=2.0, BWA>=0.7

A script to confirm all dependencies are met is here:

https://bitbucket.org/charade/svengine/raw/master/test/test_dep.sh

An example dependency install script for Mac wth Homebrew is here:

https://bitbucket.org/charade/svengine/raw/master/test/install_mac.sh

Installation Free !:

SVEngine can be used without installation as long as required commands are all in $PATH. see Examples and Manuals for more informations

Installation

You can install SVEngine as a standard package to your site python without virtualenv, in particular when all python dependencies are already met. Before you take this approach, please consider following virtualenv based installation first. The following guides were intended for Ubuntu, while Mac Homebrew user may easily adapt by removing sudo.

The other option is to use virtualenv based non-root installation, which separates svengine from site python. virtualenv command is standard with Python 2.7 or later. see: http://python-guide-pt-br.readthedocs.io/en/latest/dev/virtualenvs/. If it is not present, please see https://virtualenv.pypa.io for details to install virtualenv for your python.

sudo easy_install pip
sudo pip install virtualenv

Ask your IT manager to help install it for you if you have permission difficulties. When your system python has virtualenv, make sure your $PYTHONPATH is set to empty. Follow steps below:

sudo pip install --upgrade pip
virtualenv svengine_vpy

Now you can activate this virtual python for installing SVEngine python dependencies:

# in svengine_vpy>
source svengine_vpy/bin/activate
pip install -U scipy
pip install -U tables
pip install -U pandas
pip install -U pysam
pip install -U pybedtools
pip install -U dendropy
pip install -U biopython
pip install -U cython

Then install svengine as an standard python package:

# in svengine_vpy>
git clone https://charade@bitbucket.org/charade/svengine.git
cd svengine
git submodule update --init --recursive
test/test_dep.sh
python setup.py install

Now the SVEngine executables will be available from "$PWD/svengine_vpy/bin".

Because you installed SVEngine via virtualenv, remember to activate the virtualenv every time you use SVEngine. Also export the environmental variable $SVENGINE_BIN=$PWD/svengine_vpy/bin and add it to your $PATH.

EXECUTABLES

xwgsim -- enhanced Heng Li's wgsim

mutforge -- spiking in structure variants without fasta output

tree2var -- updating variant with a phylogenetic tree structured frequency

USAGE

By default all above executables will be available from $SVENGINE_BIN/ . Use '-h' to read script-wise usage. See Wiki pages for more details.

LICENSE

BSD3

WIKI

SVEngine's https://bitbucket.org/charade/svengine/wiki page is a growing resource for manuals, FAQs and other information. This is a MUST read place before you actually using the SVEngine tool. These documentations are also openly editable in reSructuredText format. You are more than welcome to contribute to this ongoing documentation.

CONTACT

Questions and comments shall be addressed to lixia at stanford dot edu.

CITATIONS

The SVEngine manuscript is under review. The preprint is available at BioRxiv: https://www.biorxiv.org/content/early/2018/01/12/247536