SimulaTE 1.13 – Simulating Complex Landscapes of Transposable Elements of Populations

SimulaTE 1.13

:: DESCRIPTION

SimulaTE allows to simulate arbitrary complex landscapes of transposable elements (TEs). Additionally reads may be simulated using the genomes of all indivdiuals in the population as template. Reads may be simulated using different sequencing technologies (PacBio, Illumina paired-ends) and strategies (sequencing individuals and pooled populations). SimulaTE will greatly aid in evaluating the suitability of different approaches for estimating TE abundance within populations and to test whether given genomic resources, such as a reference genome or a TE database (a fasta file containing consensus sequences of TEs), are suitable for TE identification.

::DEVELOPER

Institute of Population Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
Python

:: DOWNLOAD

SimulaTE

:: MORE INFORMATION

Citation:

SimulaTE: simulating complex landscapes of transposable elements of populations.
Kofler R.
Bioinformatics. 2018 Apr 15;34(8):1419-1420. doi: 10.1093/bioinformatics/btx772.

T-lex 2.2.2 – Assessment of Transposable Element Presence in Next-generation Sequencing data

T-lex 2.2.2

:: DESCRIPTION

The T-lex pipeline identifies reads that indicate the presence or absence of individual TEs with high specificity. Handling a large amount of data, it can return the frequency of a TE in the population.

::DEVELOPER

The Petrov Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

T-lex

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Feb 27;43(4):e22. doi: 10.1093/nar/gku1250. Epub 2014 Dec 15.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
Fiston-Lavier AS, Barrón MG, Petrov DA, González J

Fiston-Lavier AS, Carrigan M, Petrov DA and Gonzalez J.
T-LEX: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
Nuc. Acids. Res. 2011 Mar 1;39(6):e36. Epub 2010 Dec 21

RetroSeq 1.41 – Transposable Element Discovery from Next-generation sequencing data

RetroSeq 1.41

:: DESCRIPTION

RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available.

::DEVELOPER

Genomics & Genetics At The Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

RetroSeq

:: MORE INFORMATION

Citation

RetroSeq: transposable element discovery from next-generation sequencing data
Thomas M. Keane, Kim Wong and David J. Adams
Bioinformatics (2013) 29 (3): 389-390.