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

Aksamentov, Ivan and Roemer, Cornelius and Hodcroft, Emma B. and Neher, Richard A.. (2021) Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6 (67). p. 3773.

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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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Computational Modeling of Biological Processes (Neher)
UniBasel Contributors:Neher, Richard A and Aksamentov, Ivan and Römer, Cornelius
Item Type:Article, refereed
Article Subtype:Research Article
ISSN:2475-9066
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:03 Mar 2022 14:24
Deposited On:03 Mar 2022 14:24

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