ArticleMobile DNA2017
LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.
Article in Mobile DNA, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Towards targeting transposable elements for cancer therapy.Nature reviews. Cancer · 2024Review
- Detection and annotation of transposable element insertions and deletions on the human genome using nanopore sequencing.iScience · 2023Article
- Article
- TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.Genome biology · 2023Article
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic acids research · 2022Article
- Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes.International journal of molecular sciences · 2022Article
- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- InMut-finder: a software tool for insertion identification in mutagenesis using Nanopore long reads.BMC genomics · 2021Article
- Identification and Characterization of NewGenes · 2021Article
- Transposable Element Mobilization in Interspecific Yeast Hybrids.Genome biology and evolution · 2021Article
- Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster.Nucleic acids research · 2020Article
- On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements.Genes · 2019Review
- Review
- Population-specific dynamics and selection patterns of transposable element insertions in European natural populations.Molecular ecology · 2019Article
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- Transposon-Derived Non-coding RNAs and Their Function in Plants.Frontiers in plant science · 2018Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPopulation genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available. However, existing TE population genomic softwares were not designed to handle long reads and the development of new dedicated tools is needed.
resultsLoRTE 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 simulated and genuine
conclusionsLoRTE is an efficient and accurate tool to identify structural genomic variants caused by TE insertion or deletion. LoRTE is available for download at http://www.egce.cnrs-gif.fr/?p=6422.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.