ArticleMethods in molecular biology (Clifton, N.J.)2023
Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Evolutionary genomics and divergence of Cacopsylla species with a special focus on the apple proliferation vectors Cacopsylla melanoneura and Cacopsylla picta.BMC genomics · 2026Article
- Repeat-associated heterochromatin expansion in Acyclania tenebrosa, a noctuid with one of the largest lepidopteran genomes.BMC genomics · 2026Article
- Investigating the evolution of large meiotic rings of multiple X and Y sex chromosomes in two Leptodactylus frog species (Anura, Leptodactylidae).Communications biology · 2025Article
- Expansion of satellite DNAs derived from transposable elements in beetles with reduced diploid numbers.Heredity · 2025Article
- Article
- Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library.BMC genomics · 2025Article
- Comparative analysis of the mobilome yields new insights into its diversity, dynamics and evolution in parasites of the Trypanosomatidae family.Parasitology · 2025Article
- Multi-omics analysis reveals criticaliScience · 2025Article
- Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.Molecular ecology · 2024Article
- Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora.BMC genomics · 2024Article
- Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei.Genome biology and evolution · 2024Article
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Abstract
The detection and quantification of transposable elements (TE) are notoriously challenging despite their relevance in evolutionary genomics and molecular ecology. The main hurdle is caused by the dependence of numerous tools on genome assemblies, whose level of completion directly affects the comparability of the results across species or populations. dnaPipeTE, whose use is demonstrated here, tackles this issue by directly performing TE detection, classification, and quantification from unassembled short reads. This chapter details all the required steps to perform a comparative analysis of the TE content between two related species, starting from the installation of a recently containerized version of the program to the post-processing of the outputs.
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