This document lists references for Virasign and key third-party tools it depends on.
If you use Virasign in your research, please cite:
Jansen, D., & Vercauteren, K. (2026). Virasign: A viral taxonomic classification tool designed for nanopore sequencing data (v0.0.7). Zenodo. https://doi.org/10.5281/zenodo.18387008
Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal. 2014 Mar 1;239:Article 2. https://www.linuxjournal.com/content/docker-lightweight-linux-containers-consistent-development-and-deployment
Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: https://doi.org/10.1371/journal.pone.0177459.
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018 Sep 15;34(18):3094-3100. doi: https://doi.org/10.1093/bioinformatics/bty191.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-2079. doi: https://doi.org/10.1093/bioinformatics/btp352.
Li H. seqtk: Toolkit for processing sequences in FASTA/FASTQ format. https://github.com/lh3/seqtk
Steinegger M, Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat Biotechnol. 2017 Nov;35(11):1026-1028. doi: https://doi.org/10.1038/nbt.3988.
Aksamentov I, Roemer C, Hodcroft EB, Neher RA. Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software. 2021;6(67):3773. https://doi.org/10.21105/joss.03773