TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
Genome
Haplotypes
Long-read DNA sequencing
Nanopore sequencing
Software
Structural variation
Transposable element allelic frequency
Transposable element calling
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
03 04 2023
03 04 2023
Historique:
received:
21
07
2022
accepted:
23
03
2023
medline:
5
4
2023
entrez:
4
4
2023
pubmed:
5
4
2023
Statut:
epublish
Résumé
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 .
Identifiants
pubmed: 37013657
doi: 10.1186/s13059-023-02911-2
pii: 10.1186/s13059-023-02911-2
pmc: PMC10069131
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
63Informations de copyright
© 2023. The Author(s).
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