@article{fdi:010087765,
  title = {{E}fficient homology-based annotation of transposable elements using minimizers},
  author = {{G}onzalez-{G}arcia, {L}. {N}. and {L}ozano-{A}rce, {D}. and {L}ondono, {J}. {P}. and {G}uyot, {R}omain and {D}uitama, {J}.},
  editor = {},
  language = {{ENG}},
  abstract = {{P}remise{T}ransposable elements ({TE}s) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. {T}he availability of long-read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. {U}nfortunately, {TE} annotation currently represents a bottleneck in the annotation of genome assemblies. {M}ethods and {R}esults{W}e present a new functionality of the {N}ext-{G}eneration {S}equencing {E}xperience {P}latform ({NGSEP}) to perform efficient homology-based {TE} annotation. {S}equences in a reference library are treated as long reads and mapped to an input genome assembly. {A} hierarchical annotation is then assigned by homology using the annotation of the reference library. {W}e tested the performance of our algorithm on genome assemblies of different plant species, including {A}rabidopsis thaliana, {O}ryza sativa, {C}offea humblotiana, and {T}riticum aestivum (bread wheat). {O}ur algorithm outperforms traditional homology-based annotation tools in speed by a factor of three to >20, reducing the annotation time of the {T}. aestivum genome from months to hours, and recovering up to 80% of {TE}s annotated with {R}epeat{M}asker with a precision of up to 0.95. {C}onclusions{NGSEP} allows rapid analysis of {TE}s, especially in very large and {TE}-rich plant genomes.},
  keywords = {bioinformatics ; genomics ; software ; transposable elements},
  booktitle = {},
  journal = {{A}pplications in {P}lant {S}ciences},
  volume = {[{E}arly access]},
  numero = {},
  pages = {[11 p.]},
  ISSN = {2168-0450},
  year = {2023},
  DOI = {10.1002/aps3.11520},
  URL = {https://www.documentation.ird.fr/hor/fdi:010087765},
}