T-lex: A tool for fast and accurate assessment of transposable element presence in next-generation sequencing data

T-lex package

Fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements (TEs) using Next-Generation Sequencing (NGS) data.
Stanford University

How to get T-lex?
   Download T-lex
   GNU General Public License

T-lex manual pages
   T-lex2 manual
   T-lex manual

T-lex input data
   Drosophila reference genome with and w/o TEs
   Drosophila TE annotations

T-lex mailing list

   Anna-Sophie Fiston-Lavier, PhD
   Assistant Professor,
   Genomic of Adaptation - ISEM,
   University Montpellier2.
   Montpellier - FRANCE

April 2013 - T-lex on Plume

PLUME (or "Promote economicaL, Useful and Maintained softwarE for the higher education and the research communities") is a repository of software for the research community (www.projet-plume.org).You can find the T-lex description in french here.

January 2012 - T-lex version 2 (T-lex2)

T-lex2 is now available. Tlex2 returns much more accurate estimates of TE presence/absence using population NGS data compared to the original T-lex (see Manual pages). After the detection of ancestral genomic sequences, T-lex2 can reannotate individual TEs. T-lex2 also flags the putatively misannotated TE insertions.

We used T-lex2 and the DGRP data (Mackay et. al., 2012) to correct annotations for 108 TE insertions and to verify annotations for the rest (~1600) in the D. melanogaster reference genome. The reannotations and the reference genome sequence with and without TE sequences are available in the 'T-lex2 input data' page. These Tlex results will be also soon available via a dedicated database (see 'T-lex annotation').

April 2011 - T-lex version 1.1

T-lex can now tell you (i) whether the known TE insertion is present in your resequenced genome (T-lex) and (2) discover new TE insertions (T-lex de novo). T-lex has been published and is ready to use and T-lex de novo is in progress.

Note that you can run T-lex (and other scripts) on a cloud using the Scalegenomics.com next-generation cloud service. We are in the process of creating the T-lex ScaleGenomics app so that you can run T-lex without any installation hassles.

Major changes between T-lex v0.1 and T-lex v1.1:
In the presence module, the sequence identity of the contig sequence overlapping the TE sequence is now taking into account to define the presence of a TE insertion. By default, the min sequence identity required for the presence is 70% (cf. help/ option '-id').
The identity,  number of mismatches and matches are returned in the "Tresult" file.

Copyright 2011, 2012, 2013, 2014
Website designed by Anna-Sophie Fiston-Lavier
(asfiston at univ-montp2 dot fr)