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Transposome

A toolkit for annotation of transposable element families from unassembled sequence reads

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What is Transposome?

Transposome is a command line application to annotate transposable elements from paired-end whole genome shotgun data. There are many tools to estimate the mathematical nature of repeats from short sequence reads. There are also a number of tools for analyzing repeats directly from a genome assembly. This tool allows you to infer the abundance of repeat types in the genome without a reference genome sequence. The output files make it easy to quickly summarize genomic abundance by transposable element class, superfamily, family, or any other level of the repeat taxonomy.

There is also a Perl API which allows you to build custom analysis pipelines, repeat stages of the analysis, or test a range of parameter values for each phase of Transposome (see the API Tutorial page for more information).

DEPENDENCIES

To use Transposome, you will need Perl installed (version 5.10 or greater) and it is very simple to install Perl with a tool called perlbrew. A step-by-step set of instructions is provided for installing a recent version of Perl. That wiki page also explains the commands below.

INSTALLATION

Note that the following commands assume a fresh cloud instance with no compilers or libraries installed. There are only a couple of steps, but please be advised that it can take a little while (perhaps 20 minutes) to compile the dependencies.

For Ubuntu/Debian as the OS:

apt-get install -y build-essential lib32z1 git ncbi-blast+
curl -L cpanmin.us | perl - git://github.com/sestaton/Transposome.git

For RHEL/Fedora:

yum groupinstall "Development Tools"
yum install -y glibc.i686 gcc-c++ git ncbi-blast+
curl -L cpanmin.us | perl - git://github.com/sestaton/Transposome.git

If you run into issues, it may be easier to download the latest release and install manually (see the troubleshooting page for more information) with the following commands.

tar xzf Transposome.tar.gz
cd Transposome
perl Makefile.PL
make
make test
make install

Updating your installation can be achieved by simply running the same commands. Please report any issues.

BASIC USAGE

Following installation, get the Transposome configuration file:

curl -L tr.im/transposomeconfig > transposome_config.yml

Next, edit the configuration file by specifying the location of data files and parameters for analysis. Note that if you downloaded manually, a configuration file can be found in the 'config' directory, or the configuration file on the Quick Start page can be copied into a text editor and saved locally. It makes no difference which way you create the configuration file, though the curl method is faster.

Then, simply run the transposome program, specifying your configuration file:

transposome --config transposome_config.yml

The name of the configuration file does not matter, this is just an example. Though, the format is important. See the Quick Start wiki page for more details.

ADVANCED USAGE

It is possible to run only one part of the Transposome package, the clustering methods for example, or create your own analysis methods to plug into Transposome. In addition, you can extend existing methods.

For all available methods, simply type perldoc followed by the name of the class you are interested in using. For example,

perldoc Transposome::Cluster

Available classes are:

Transposome::Annotation
Transposome::Cluster
Transposome::PairFinder
Transposome::SeqFactory
Transposome::SeqUtil
Transposome::Run::Blast

SUPPORT AND DOCUMENTATION

After installing, you can find documentation for the Transposome package with the perldoc command.

perldoc Transposome

If you are not interested in using Transposome programmatically or inspecting the class methods, simply type perldoc followed by the name of main program to run the full analysis.

perldoc transposome 

The transposome program will also print a diagnostic help message when executed with no arguments.

You can also look for information at:

Transposome wiki
    https://github.com/sestaton/Transposome/wiki

Transposome issue tracker
    https://github.com/sestaton/Transposome/issues

CITATION

Transposome is published in the journal Bioinformatics, and if you use this software in your work please use the following citation:

Staton SE, and Burke JM. 2015. Transposome: Annotation of transposable element families
     from unassembled sequence reads. Bioinformatics, doi: 10.1093/bioinformatics/btv05

LICENSE AND COPYRIGHT

Copyright (C) 2013-2015 S. Evan Staton

This program is distributed under the MIT (X11) License, which should be distributed with the package. If not, it can be found here: http://www.opensource.org/licenses/mit-license.php

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