Mze N. P. auteur aut IRD Beye M. auteur aut IRD Kacel I. auteur aut IRD Tola R. auteur aut IRD Basco Leonardo auteur aut IRD Bogreau H. auteur aut IRD Colson P. auteur aut IRD Fournier P. E. auteur aut IRD text journalArticle eng text/pdf reformatted digital access In the present study, we propose a high-throughput sequencing protocol using aNextera XT Library DNA kit on an Illumina MiSeq instrument. We made major modifications to this library preparation in order to multiplex 384 samples in a single Illumina flow cell. To validate our protocol, we compared the sequences obtained with the modified Illumina protocol to those obtained with the GridION Nanopore protocol. For the modified Illumina 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. For the GridION Nanopore 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. The modified Illumina 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 Illumina protocol. Our modified MiSeq protocol yields similar genome sequence data as the GridION Nanopore protocol and has the advantage of being able to handle four times more samples simultaneously and hence is much less expensive. specialized Illumina MiSeq SARS-CoV-2 next-generation sequencing genomics sequence analysis 052 020 13 9 1648 [9 ] 2022 https://www.documentation.ird.fr/hor/fdi:010086108 10.3390/genes13091648 [F B010086108] https://www.documentation.ird.fr/hor/fdi:010086108 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2022-11/010086108.pdf IRD - Base Horizon / Pleins textes 2022-11-09 2025-02-24 fdi:010086108 fre