ArticleNucleic acids research2011
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies.Plant biotechnology journal · 2025Article
- Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing.Genome biology · 2025Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.Genome biology · 2023Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A sensitive repeat identification framework based on short and long reads.Nucleic acids research · 2021Article
- T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data.Bioinformatics (Oxford, England) · 2020Article
- A unique cluster ofMobile DNA · 2019Article
- Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in theG3 (Bethesda, Md.) · 2018Article
- The case for not masking away repetitive DNA.Mobile DNA · 2018Article
- Deep sequencing of natural and experimental populations ofGenome research · 2017Article
- Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes.Genome biology and evolution · 2017Article
- McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data.G3 (Bethesda, Md.) · 2017Article
- Article
- Genomics of Parallel Experimental Evolution in Drosophila.Molecular biology and evolution · 2017Article
- Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae.Genetics · 2016Article
- A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.BMC genomics · 2016Article
- Article
- Unique transposon landscapes are pervasive across Drosophila melanogaster genomes.Nucleic acids research · 2015Article
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Authors and funding
4 authors.
Funding
Abstract
Transposable elements (TEs) are repetitive DNA sequences that are ubiquitous, extremely abundant and dynamic components of practically all genomes. Much effort has gone into annotation of TE copies in reference genomes. The sequencing cost reduction and the newly available next-generation sequencing (NGS) data from multiple strains within a species offer an unprecedented opportunity to study population genomics of TEs in a range of organisms. Here, we present a computational pipeline (T-lex) that uses NGS data to detect the presence/absence of annotated TE copies. T-lex can use data from a large number of strains and returns estimates of population frequencies of individual TE insertions in a reasonable time. We experimentally validated the accuracy of T-lex detecting presence or absence of 768 previously identified TE copies in two resequenced Drosophila melanogaster strains. Approximately 95% of the TE insertions were detected with 100% sensitivity and 97% specificity. We show that even at low levels of coverage T-lex produces accurate results for TE copies that it can identify reliably but that the rate of 'no data' calls increases as the coverage falls below 15×. T-lex is a broadly applicable and flexible tool that can be used in any genome provided the availability of the reference genome, individual TE copy annotation and NGS data.
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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.