A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater

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.

Benchmarking

SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

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.

Unlocking capacities of viral genomics for the COVID-19 pandemic response

no code implementations • 28 Apr 2021 • Sergey Knyazev, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh, Smruthi Karthikeyan, Dhrithi Deshpande, Zoia Comarova, Angela Lu, Yuri Porozov, Aiping Wu, Malak Abedalthagafi, Shivashankar Nagaraj, Adam Smith, Pavel Skums, Jason Ladner, Tommy Tsan-Yuk Lam, Nicholas Wu, Alex Zelikovsky, Rob Knight, Keith Crandall, Serghei Mangul

More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to recent advances in high-throughput sequencing technologies, the rapid global spread of SARS-CoV-2, and its persistent threat to public health.

Technology dictates algorithms: Recent developments in read alignment

2 code implementations • 28 Feb 2020 • Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul

We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques.