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LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

Eric Disdero, Jonathan Filée
doi: https://doi.org/10.1101/073551
Eric Disdero
Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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Jonathan Filée
Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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Abstract

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

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 05, 2016.
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LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
Eric Disdero, Jonathan Filée
bioRxiv 073551; doi: https://doi.org/10.1101/073551
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LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
Eric Disdero, Jonathan Filée
bioRxiv 073551; doi: https://doi.org/10.1101/073551

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