Accessible viral metagenomics for public health and clinical domains with Jovian

Munnink, B. B. O. et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat. Med. 26, 1405–1411 (2020).Article 

Google Scholar 
Houldcroft, C. J., Beale, M. A. & Breuer, J. Clinical and biological insights from viral genome sequencing. Nat. Rev. Microbiol. 15, 183–192 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Grubaugh, N. D. et al. Tracking virus outbreaks in the twenty-first century. Nat. Microbiol. 4, 10–19 (2019).Article 
CAS 
PubMed 

Google Scholar 
Francis, R. V. et al. The impact of real-time whole-genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks. J. Infect. Dis. 225, 10–18 (2022).Article 
CAS 
PubMed 

Google Scholar 
Chiu, C. Y. & Miller, S. A. Clinical metagenomics. Nat. Rev. Genet. 20, 341–355 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Vilsker, M. et al. Genome detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics 35, 871–873 (2019).Article 
CAS 
PubMed 

Google Scholar 
Minot, S. S., Krumm, N. & Greenfield, N. B. One codex: a sensitive and accurate data platform for genomic microbial identification. BioRxiv 027607 (2015).Flygare, S. et al. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol. 17, 1–18 (2016).Article 

Google Scholar 
Taxonomer. Taxonomer Page. https://taxonomer.iobio.io/ (Accessed 02 November 2023).Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 1–13 (2019).Article 

Google Scholar 
Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721–1729 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Cadenas-Castrejón, E., Verleyen, J., Boukadida, C., Díaz-González, L. & Taboada, B. Evaluation of tools for taxonomic classification of viruses. Brief. Funct. Genom. 22, 31–41 (2023).Article 

Google Scholar 
Kroneman, A. et al. Proposal for a unified norovirus nomenclature and genotyping. Arch. Virol. 158, 2059–2068 (2013).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Kroneman, A. et al. An automated genotyping tool for enteroviruses and noroviruses. J. Clin. Virol. 51, 121–125 (2011).Article 
CAS 
PubMed 

Google Scholar 
Kroneman, A., de Sousa, R., Verhoef, L., Koopmans, M. P. & Vennema, H. Usability of the international HAVNet hepatitis a virus database for geographical annotation, backtracing and outbreak detection. Eurosurveillance 23, 1700802 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Mulder, A. C. et al. HEVnet: a one health, collaborative, interdisciplinary network and sequence data repository for enhanced hepatitis E virus molecular typing, characterisation and epidemiological investigations. Eurosurveillance 24, 1800407 (2019).Article 
PubMed 
PubMed Central 

Google Scholar 
Wilkinson, M. D. et al. The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3, 1–9 (2016).Article 

Google Scholar 
Jansen, S. A. et al. Broad virus detection and variant discovery in fecal samples of hematopoietic transplant recipients using targeted sequence capture metagenomics. Front. Microbiol. 11, 560179 (2020).Article 
PubMed 
PubMed Central 

Google Scholar 
Carbo, E. C. et al. Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics. J. Clin. Virol. 130, 104566 (2020).Article 
CAS 
PubMed 

Google Scholar 
Köster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 28, 2520–2522 (2012).Article 
PubMed 

Google Scholar 
Grüning, B. et al. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat. Methods 15, 475–476 (2018).Article 
PubMed 
PubMed Central 

Google Scholar 
Kurtzer, G. M., Sochat, V. & Bauer, M. W. Singularity: scientific containers for mobility of compute. PLoS ONE 12, e0177459 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data (2010).Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047–3048 (2016).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Schneider, V. A. et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 27, 849–864 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).Article 
PubMed 
PubMed Central 

Google Scholar 
Broad Institute. Broad Institute GitHub Page for Picard. https://broadinstitute.github.io/picard/ (Accessed 06 October 2023).Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wheeler, D. L. et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 36, D13–D21 (2007).Article 
ADS 
PubMed 
PubMed Central 

Google Scholar 
Rubino, F. & Creevey, C. MGkit Metagenomic framework for the study of microbial communities. Figshare Poste (2014).NCBI. NCBI FTP for new_taxdump. https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/ (Accessed 06 October 2023).Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bushnell, B. BBTools Software Package (2014).Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Wilm, A. et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 40, 11189–11201 (2012).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Mihara, T. et al. Linking virus genomes with host taxonomy. Viruses 8, 66 (2016).Article 
PubMed 
PubMed Central 

Google Scholar 
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 1–11 (2010).Article 

Google Scholar 
Quantopian. Quantopian GitHub Page. https://github.com/quantopian/qgrid (Accessed 06 October 2023).Bokeh. Bokeh Homepage. https://bokeh.pydata.org/en/latest/ (Accessed 06 October 2023).Ondov, B. D., Bergman, N. H. & Phillippy, A. M. Interactive metagenomic visualization in a web browser. BMC Bioinform. 12, 1–10 (2011).Article 

Google Scholar 
Robinson, J. T., Thorvaldsdóttir, H., Turner, D. & Mesirov, J. P. igv.js: an embeddable JavaScript implementation of the integrative genomics viewer (IGV). Bioinformatics 39, 830 (2023).Article 

Google Scholar 
Kluyver, T. et al. Positioning and Power in Academic Publishing: Players, Agents and Agendas 87–90 (IOS, 2016).Ragan-Kelley, B. et al. Proceedings of the 17th Python in Science Conference 113–120 (eds. Akici, F.).IBM. IBM Spectrum LSF Suites Homepage. https://www.ibm.com/products/hpc-workload-management (Accessed 06 October 2023).Sched, M. D. Slurm Homepage. https://www.schedmd.com/ (Accessed 06 October 2023).Schmitz, D. et al. Metagenomic surveillance of viral gastroenteritis in a public health setting. Microbiol. Spectr. 11, e05022 (2023).Article 
PubMed 
PubMed Central 

Google Scholar 
Rivest, R. (Editor RFC, 1992).Fitzpatrick, P. daff GitHub Page. https://github.com/paulfitz/daff (Accessed 06 October 2023).de Vries, J. J. et al. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. J. Clin. Virol. 138, 104812 (2021).Article 
PubMed 

Google Scholar 
Brinkmann, A. et al. Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing data sets. J. Clin. Microbiol. 57, 419. https://doi.org/10.1128/jcm.00466-00419 (2019).Article 

Google Scholar 
de Vries, J. J. et al. Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples. J. Clin. Virol. 141, 104908 (2021).Article 
PubMed 
PubMed Central 

Google Scholar 
Nieroda, L. et al. iRODS metadata management for a cancer genome analysis workflow. BMC Bioinform. 20, 1–8 (2019).Article 

Google Scholar 
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 1–12 (2014).Article 

Google Scholar 
Kulakov, L. A., McAlister, M. B., Ogden, K. L., Larkin, M. J. & O’Hanlon, J. F. Analysis of bacteria contaminating ultrapure water in industrial systems. Appl. Environ. Microbiol. 68, 1548–1555 (2002).Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar 
iRODS. iRODS Homepage. https://irods.org/ (Accessed 06 October 2023).Bodewes, R. et al. Molecular epidemiology of mumps viruses in the Netherlands, 2017–2019. PLoS ONE 15, e0233143 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Benschop, K. S. et al. Molecular epidemiology and evolutionary trajectory of emerging Echovirus 30, Europe. Emerg. Infect. Dis. 27, 1616 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Amid, C. et al. The COMPARE data hubs. Database 2019, 136 (2019).RIVM Bioinformatics Team. Juno GitHub Page. https://github.com/RIVM-bioinformatics/juno-assembly (Accessed 06 October 2023).