Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences Ortuño Guzmán, Francisco Manuel Loucera, Carlos Casimiro-Soriguer, Carlos S. Lepe, Jose Antonio Camacho, Pedro Merino, Laura de Salazar, Adolfo Chueca, Natalia García, Federico Pérez Florido, Javier Dopazo, Joaquin Background: The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data. Results: We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (<20%). Conclusions: Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing. 2025-01-29T11:48:35Z 2025-01-29T11:48:35Z 2021-12-02 journal article Francisco M Ortuño, Carlos Loucera, Carlos S Casimiro-Soriguer, Jose A Lepe, Pedro Camacho Martinez, Laura Merino Diaz, Adolfo de Salazar, Natalia Chueca, Federico García, Javier Perez-Florido, Joaquin Dopazo, Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences, GigaScience, Volume 10, Issue 12, December 2021, giab078, doi:10.1093/gigascience/giab078 https://hdl.handle.net/10481/100949 10.1093/gigascience/giab078 eng http://creativecommons.org/licenses/by-nc-nd/3.0/ open access Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License Oxford Academic