@article{fdi:010086108,
  title = {{S}imultaneous {SARS}-{C}o{V}-2 genome sequencing of 384 samples on an {I}llumina {M}i{S}eq instrument through protocol optimization},
  author = {{M}ze, {N}. {P}. and {B}eye, {M}. and {K}acel, {I}. and {T}ola, {R}. and {B}asco, {L}eonardo and {B}ogreau, {H}. and {C}olson, {P}. and {F}ournier, {P}. {E}.},
  editor = {},
  language = {{ENG}},
  abstract = {{I}n the present study, we propose a high-throughput sequencing protocol using a{N}extera {XT} {L}ibrary {DNA} kit on an {I}llumina {M}i{S}eq instrument. {W}e made major modifications to this library preparation in order to multiplex 384 samples in a single {I}llumina flow cell. {T}o validate our protocol, we compared the sequences obtained with the modified {I}llumina protocol to those obtained with the {G}rid{ION} {N}anopore protocol. {F}or the modified {I}llumina protocol, our results showed that 94.9% (357/376) of the sequences were interpretable, with a viral genome coverage between 50.5% and 99.9% and an average depth of 421x. {F}or the {G}rid{ION} {N}anopore protocol, 94.6% (356/376) of the sequences were interpretable, with a viral genome coverage between 7.0% and 98.6% and an average depth of 2123x. {T}he modified {I}llumina protocol allows for gaining {EUR} 4744 and returning results of 384 samples in 53.5 h versus four times 55.5 h with the standard {I}llumina protocol. {O}ur modified {M}i{S}eq protocol yields similar genome sequence data as the {G}rid{ION} {N}anopore protocol and has the advantage of being able to handle four times more samples simultaneously and hence is much less expensive.},
  keywords = {{I}llumina {M}i{S}eq ; {SARS}-{C}o{V}-2 ; next-generation sequencing ; genomics ; sequence analysis},
  booktitle = {},
  journal = {{G}enes},
  volume = {13},
  numero = {9},
  pages = {1648 [9 ]},
  year = {2022},
  DOI = {10.3390/genes13091648},
  URL = {https://www.documentation.ird.fr/hor/fdi:010086108},
}