@article{fdi:010087606,
  title = {{T}r{EMOLO} : accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches},
  author = {{M}ohamed, {M}. and {S}abot, {F}ran{\c{c}}ois and {V}aroqui, {M}. and {M}ugat, {B}. and {A}udouin, {K}. and {P}elisson, {A}. and {F}iston-{L}avier, {A}. {S}. and {C}hambeyron, {S}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ransposable {E}lement {MO}nitoring with {LO}ng-reads ({T}r{EMOLO}) is a new software that combines assembly- and mapping-based approaches to robustly detect genetic elements called transposable elements ({TE}s). {U}sing high- or low-quality genome assemblies, {T}r{EMOLO} can detect most {TE} insertions and deletions and estimate their allele frequency in populations. {B}enchmarking with simulated data revealed that {T}r{EMOLO} outperforms other state-of-the-art computational tools. {TE} detection and frequency estimation by {T}r{EMOLO} were validated using simulated and experimental datasets. {T}herefore, {T}r{EMOLO} is a comprehensive and suitable tool to accurately study {TE} dynamics. {T}r{EMOLO} is available under {GNU} {GPL}3.0 at https://github.com/{D}rosophila {G}enome{E}volution/{T}r{EMOLO}.},
  keywords = {{G}enome ; {S}oftware ; {T}ransposable element calling ; {L}ong-read {DNA} ; sequencing ; {N}anopore sequencing ; {T}ransposable element allelic frequency ; {H}aplotypes ; {S}tructural variation},
  booktitle = {},
  journal = {{G}enome {B}iology},
  volume = {24},
  numero = {1},
  pages = {63 [20 ]},
  ISSN = {1474-760{X}},
  year = {2023},
  DOI = {10.1186/s13059-023-02911-2},
  URL = {https://www.documentation.ird.fr/hor/fdi:010087606},
}