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

Abstract

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. Statement of need After assembly of a consensus genome from raw read data, it is usually desirable to (i) assess the quality of the sequence, (ii) assign it to a known clade or type, and (iii) compare it to a reference sequence to detect evolutionary changes. Nextclade addresses this need through a command-line interface for bulk analysis of many sequences and a web-tool with the same functionality coupled to an interactive visualization. Nextclade is built on Nextalign, a codon-aware pairwise sequence aligner for similar viral genomes, which allows unambiguous calling of amino-acid changes associated with changes in the nucleotide sequence. The sequence is then placed onto a phylogenetic tree generated by the augur pipeline (Huddleston et al., 2021) of the Nextstrain tool-chain (Hadfield et al., 2018). During the SARS-CoV-2 pandemic, Nextclade has already allowed countless users to quickly analyze their data, assign sequences to clades and variants of concern, and identify mutations of interest.