no code implementations • 29 Sep 2023 • Viorel Munteanu, Victor Gordeev, Michael Saldana, Eva Aßmann, Justin Maine Su, Nicolae Drabcinski, Oksana Zlenko, Maryna Kit, Felicia Iordachi, Khooshbu Kantibhai Patel, Abdullah Al Nahid, Likhitha Chittampalli, Yidian Xu, Pavel Skums, Shelesh Agrawal, Martin Hölzer, Adam Smith, Alex Zelikovsky, Serghei Mangul
Here, we perform comprehensive benchmarking of 18 bioinformatics methods for estimating the relative abundance of SARS-CoV-2 (sub)lineages in wastewater by using data from 36 in vitro mixtures of synthetic lineage and sublineage genomes.
no code implementations • 23 Sep 2023 • Viorel Munteanu, Michael Saldana, Dumitru Ciorba, Viorel Bostan, Justin Maine Su, Nadiia Kasianchuk, Nitesh Kumar Sharma, Sergey Knyazev, Victor Gordeev, Eva Aßmann, Andrei Lobiuc, Mihai Covasa, Keith A. Crandall, Wenhao O. Ouyang, Nicholas C. Wu, Christopher Mason, Braden T Tierney, Alexander G Lucaci, Alex Zelikovsky, Fatemeh Mohebbi, Pavel Skums, Cynthia Gibas, Jessica Schlueter, Piotr Rzymski, Helena Solo-Gabriele, Martin Hölzer, Adam Smith, Serghei Mangul
The existing bioinformatics tools used to analyze wastewater sequencing data are often based on previously developed methods for quantifying the expression of transcripts or viral diversity.