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

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.

Long-range single-molecule mapping of chromatin modification in eukaryotes

“…Compared with ChIP-seq, the BIND&MODIFY significantly improves the unique mapping rate (Supplemental Figure 11), by taking advantage of long-range sequencing, which generates read length that may span the entire length of full transposon and avoid multiple mapping issues. With the advantages, the long-range sequencing was also used to identify the novel transposon deletion and insertions 47 . There were minimal studies about the H3K27me3 on retrotransposons 48 .…”

Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses?

“…Of course, as soon as these technologies will become the new standard, the current tools for TE analyses will become obsolete and new methodological procedures will need to be developed. In this way, a bioinformatic tool has recently been proposed to determine the presence/absence of TE insertions using reads produced by the PacBio technology (LorTE, (Disdero and Filée 2017)).…”