I designed the T-lex package that is a computational tool to annotate individual transposable element (TE) insertions in strains or population using next-generation sequencing (NGS) data. The original version of the T-lex pipeline has been published (Fiston-Lavier et al. 2011 NAR). This version included a pipeline to call the presence and/or absence of individual annotated TE insertions. I redesigned this pipeline to handle paired-end data of individual and pooled sample. The new version of the T-lex presence/absence pipeline is available at http://petrov.stanford.edu/cgi-bin/Tlex.html.
T-lex2 is now composed of two pipelines. Both pipelines combine single or paired-end read mapping with the read depth coverage information and handle individual or pooled sample.
The paper of version 2 of the T-lex package including the T-lex de novo pipeline should come out soon.
(A) The “presence/absence” pipeline can be used to call individual TE insertions annotated in a reference sequence by determining their presence and/or absence in strains sequenced. This pipeline can be also used to annotate the TSD (Target Site Duplication) of individual TE insertions. Combining calls from several strains from a same population, the "presence/absence" pipeline can estimate the population frequency of each TE insertion.
(B) The “de novo” pipeline can be used to discover and annotate TE insertions not annotated in the reference sequence.
T-lex is in active development with the help of the T-lex team (contact afiston [at] stanford [dot] edu).
- Anna-Sophie Fiston-Lavier,
- Maite Barron - PhD student,
- Barrientos Mauricio - master student,
- Vippala Lokitha - master student,
- Dave Tushar - master student,
- Matthew Carrigan - undergraduate student.
- Dmitri Petrov - Professor @ Stanford University,
- Josefa Gonzalez - Group leader @ Institute of Evolutionary Biology,
- Aleksandr Arhipov - admin system @ ScaleGenomics.