PT  - JOURNAL ARTICLE
AU  - Eric Disdero
AU  - Jonathan Filée
TI  - LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
AID  - 10.1101/073551
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 073551
4099  - http://biorxiv.org/content/early/2016/09/05/073551.short
4100  - http://biorxiv.org/content/early/2016/09/05/073551.full
AB  - Motivation Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when short read sequences technology is used.Results LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tools to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences.Availability and Implementation LoRTE is available at http://www.egce.cnrs-gif.fr/?p=6422. It is written in Python 2.7 and only requires the NCBI BLAST + package. LoRTE can be used on standard computer with limited RAM resources and reasonable running time even with large datasets.Contact jonathan.filee{at}ecge.cnrs-gif.fr