Nextclade: clade assignment, mutation calling and quality control for viral genomes

• DOI: 10.21105/joss.03773
• Publication Date: 2021-11-30T18:19:49Z
• Authors: Ivan Aksamentov; Cornelius Roemer; Emma Hodcroft; Richard Neher
• Keywords: 0301 basic medicine; 0303 health sciences; 03 medical and health sciences; Genomic epidemiology; 3. Good health

available at https://clades.nextstrain.org<br/>The variants of concern (VoCs) of SARS-CoV-2 have highlighted the need for a global molecular surveillance of pathogens via whole genome sequencing. Such sequencing, for SARS-CoV-2 and other pathogens, is performed by an ever increasing number of labs across the globe, resulting in an increased need for an easy, fast, and decentralized analysis of initial data. Nextclade aligns viral genomes to a reference sequence, calculates several quality control (QC) metrics, assigns sequences to a clade or variant, and identifies changes in the viral proteins relative to the reference sequence. Nextclade is available as a command-line tool and as a web application with completely client based processing, meaning that sequence data doesn't leave the user's browser.<br/>