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Found 5 papers, 1 papers with code
A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
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.
SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities
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.
Antigenic cooperation in Viral Populations: Transformation of Functions of Intra-Host Viral Variants
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by continuous genomic diversification and allows to explain a number of experimental observations associated with the establishment of chronic infections by highly mutable viruses.
Unlocking capacities of viral genomics for the COVID-19 pandemic response
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
We separately discuss how longer read lengths produce unique advantages and limitations to read alignment techniques.
