ArticleGenome biology2023
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Review
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila melanogaster genome.Nucleic acids research · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector.Scientific reports · 2025Article
- 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
- The histone demethylase dLsd1 regulates organ size by silencing transposable elements.Communications biology · 2025Article
- A unified framework to analyze transposable element insertion polymorphisms using graph genomes.Nature communications · 2024Article
- Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis.Nucleic acids research · 2024Article
- Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics.Nature chemistry · 2024Review
- 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
- TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.Genome biology · 2023Article
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Authors and funding
8 authors.
Funding
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Abstract
Transposable Element MOnitoring with LOng-reads (TrEMOLO) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements (TEs). Using high- or low-quality genome assemblies, TrEMOLO can detect most TE insertions and deletions and estimate their allele frequency in populations. Benchmarking with simulated data revealed that TrEMOLO outperforms other state-of-the-art computational tools. TE detection and frequency estimation by TrEMOLO were validated using simulated and experimental datasets. Therefore, TrEMOLO is a comprehensive and suitable tool to accurately study TE dynamics. TrEMOLO is available under GNU GPL3.0 at https://github.com/DrosophilaGenomeEvolution/TrEMOLO .
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