The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Nextclade: clade assignment, mutation calling and quality control for viral genomes
Open accessAbstract
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.
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Citations
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
Nextstrain: real-time tracking of pathogen evolution
Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty407 · Cited by 3,154
Self-citation
Cited by
COVID‐19 severity from Omicron and Delta SARS‐CoV‐2 variants
Wrenn, J. O., Pakala, S. B., Vestal, G., Shilts, M. H., Brown, H. M., Bowen, S. M., Strickland, B. A., Williams, T., Mallal, S. A., Jones, I. D., et al. (2022) · Influenza and Other Respiratory Viruses · doi:10.1111/irv.12982 · Cited by 99
Fonager, J., Bennedbæk, M., Bager, P., Wohlfahrt, J., Ellegaard, K. M., Ingham, A. C., Edslev, S. M., Stegger, M., Sieber, R. N., Lassauniere, R., et al. (2022) · Eurosurveillance · doi:10.2807/1560-7917.es.2022.27.10.2200181 · Cited by 78
Wang, W., Lusvarghi, S., Subramanian, R., Epsi, N. J., Wang, R., Goguet, E., Fries, A. C., Echegaray, F., Vassell, R., Coggins, S., et al. (2022) · doi:10.1101/2022.07.05.498883 · Cited by 68
Metadata
- Authors
- Aksamentov, I., Roemer, C., Hodcroft, E., & Neher, R.
- Venue
- Journal of Open Source Software
- Publisher
- The Open Journal
- Published
- 2021-11-30
- Volume
- 6
- Issue
- 67
- Pages
- 3773
- ISSN
- 2475-9066 (ISSN-L)
- OpenAlex
- W3215610096
- Cited by
- 1,046
- References
- 3
- FWCI
- 44.81
- Type
- journal article
- Language
- en
- Open access
- diamond
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- Aksamentov, I., Roemer, C., Hodcroft, E., & Neher, R. (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software. https://doi.org/10.21105/joss.03773
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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