Viruses, Vol. 16, Pages 430: Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows

Viruses, Vol. 16, Pages 430: Recommendations for Uniform Variant Calling of SARS-CoV-2 Genome Sequence across Bioinformatic Workflows Viruses doi: 10.3390/v16030430 Authors: Ryan Connor Migun Shakya David A. Yarmosh Wolfgang Maier Ross Martin Rebecca Bradford J. Rodney Brister Patrick S. G. Chain Courtney A. Copeland Julia di Iulio Bin Hu Philip Ebert Jonathan Gunti Yumi Jin Kenneth S. Katz Andrey Kochergin Tré LaRosa Jiani Li Po-E Li Chien-Chi Lo Sujatha Rashid Evguenia S. Maiorova Chunlin Xiao Vadim Zalunin Lisa Purcell Kim D. Pruitt Genomic sequencing of clinical samples to identify emerging variants of SARS-CoV-2 has been a key public health tool for curbing the spread of the virus. As a result, an unprecedented number of SARS-CoV-2 genomes were sequenced during the COVID-19 pandemic, which allowed for rapid identification of genetic variants, enabling the timely design and testing of therapies and deployment of new vaccine formulations to combat the new variants. However, despite the technological advances of deep sequencing, the analysis of the raw sequence data generated globally is neither standardized nor consistent, leading to vastly disparate sequences that may impact identification of variants. Here, we show that for both Illumina and Oxford Nanopore sequencing platforms, downstream bioinformatic protocols used by industry, government, and academic groups resulted in different virus sequences from same sam...
Source: Viruses - Category: Virology Authors: Tags: Article Source Type: research