{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T07:08:32Z","timestamp":1783926512689,"version":"3.55.0"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T00:00:00Z","timestamp":1704844800000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UC San Diego Faculty Research Funds"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The genomic surveillance of viral pathogens such as SARS-CoV-2 and HIV-1 has been critical to modern epidemiology and public health, but the use of sequence analysis pipelines requires computational expertise, and web-based platforms require sending potentially sensitive raw sequence data to remote servers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce ViralWasm, a user-friendly graphical web application suite for viral genomics. All ViralWasm tools utilize WebAssembly to execute the original command line tools client-side directly in the web browser without any user setup, with a cost of just 2-3x slowdown with respect to their command line counterparts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The ViralWasm tool suite can be accessed at: https:\/\/niema-lab.github.io\/ViralWasm<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae018","type":"journal-article","created":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T21:59:59Z","timestamp":1704837599000},"source":"Crossref","is-referenced-by-count":8,"title":["ViralWasm: a client-side user-friendly web application suite for viral genomics"],"prefix":"10.1093","volume":"40","author":[{"given":"Daniel","family":"Ji","sequence":"first","affiliation":[{"name":"Department of Computer Science & Engineering, UC San Diego , La Jolla, CA 92093, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Aboukhalil","sequence":"additional","affiliation":[{"name":"Chan Zuckerberg Initiative , Redwood City, CA 94063, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2209-8128","authenticated-orcid":false,"given":"Niema","family":"Moshiri","sequence":"additional","affiliation":[{"name":"Department of Computer Science & Engineering, UC San Diego , La Jolla, CA 92093, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,1,10]]},"reference":[{"key":"2024012514035046600_btae018-B1","doi-asserted-by":"crossref","first-page":"100190","DOI":"10.1016\/j.health.2023.100190","article-title":"A comprehensive review and conceptual framework for cloud computing adoption in bioinformatics","volume":"3","author":"Banimfreg","year":"2023","journal-title":"Healthc Anal"},{"key":"2024012514035046600_btae018-B2","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2024012514035046600_btae018-B3","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2024012514035046600_btae018-B4","doi-asserted-by":"crossref","first-page":"758","DOI":"10.3390\/v12070758","article-title":"Validation of variant assembly using HAPHPIPE with Next-Generation sequence data from viruses","volume":"12","author":"Gibson","year":"2020","journal-title":"Viruses"},{"key":"2024012514035046600_btae018-B5","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13059-018-1618-7","article-title":"An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar","volume":"20","author":"Grubaugh","year":"2019","journal-title":"Genome Biol"},{"key":"2024012514035046600_btae018-B6","first-page":"185","author":"Haas","year":"2017"},{"key":"2024012514035046600_btae018-B7","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/molbev\/msy016","article-title":"HIV-TRACE (TRAnsmission cluster engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens","volume":"35","author":"Kosakovsky Pond","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2024012514035046600_btae018-B8","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2024012514035046600_btae018-B9","doi-asserted-by":"crossref","first-page":"e98443","DOI":"10.1371\/journal.pone.0098443","article-title":"Using HIV networks to inform real time prevention interventions","volume":"9","author":"Little","year":"2014","journal-title":"PLoS ONE"},{"key":"2024012514035046600_btae018-B10","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1093\/bioinformatics\/btaa743","article-title":"ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes","volume":"37","author":"Moshiri","year":"2021","journal-title":"Bioinformatics"},{"key":"2024012514035046600_btae018-B11","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btad317","article-title":"ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data","volume":"39","author":"Moshiri","year":"2023","journal-title":"Bioinformatics"},{"key":"2024012514035046600_btae018-B12","doi-asserted-by":"crossref","first-page":"5077","DOI":"10.1038\/s41598-022-09035-w","article-title":"The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction","volume":"12","author":"Moshiri","year":"2022","journal-title":"Sci Rep"},{"key":"2024012514035046600_btae018-B13","doi-asserted-by":"crossref","first-page":"e12129","DOI":"10.7717\/peerj.12129","article-title":"VGEA: an RNA viral assembly toolkit","volume":"9","author":"Oluniyi","year":"2021","journal-title":"PeerJ"},{"key":"2024012514035046600_btae018-B14","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1093\/bioinformatics\/btab015","article-title":"V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data","volume":"37","author":"Posada-C\u00e9spedes","year":"2021","journal-title":"Bioinformatics"},{"key":"2024012514035046600_btae018-B15","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"Price","year":"2010","journal-title":"PLoS ONE"},{"key":"2024012514035046600_btae018-B199701","doi-asserted-by":"crossref","first-page":"e481","DOI":"10.1016\/S2666-5247(21)00121-X","article-title":"Genomic surveillance to combat COVID-19: challenges and opportunities","volume":"2","author":"Robishaw","year":"2021","journal-title":"The Lancet Microbe"},{"key":"2024012514035046600_btae018-B16","first-page":"1","author":"Spies","year":"2021"},{"key":"2024012514035046600_btae018-B17","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees","volume":"10","author":"Tamura","year":"1993","journal-title":"Mol Biol Evol"},{"key":"2024012514035046600_btae018-B18","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"The Galaxy Community","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024012514035046600_btae018-B19","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1093\/sysbio\/syv068","article-title":"Fast dating using least-squares criteria and algorithms","volume":"65","author":"To","year":"2016","journal-title":"Syst Biol"},{"key":"2024012514035046600_btae018-B20","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/s12859-021-04294-2","article-title":"HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences","volume":"22","author":"Truong Nguyen","year":"2021","journal-title":"BMC Bioinform"},{"key":"2024012514035046600_btae018-B21","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1093\/bioinformatics\/bty695","article-title":"Genome detective: an automated system for virus identification from high-throughput sequencing data","volume":"35","author":"Vilsker","year":"2019","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae018\/55399615\/btae018.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/1\/btae018\/56416837\/btae018.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/1\/btae018\/56416837\/btae018.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,25]],"date-time":"2024-01-25T17:01:32Z","timestamp":1706202092000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae018\/7515252"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,1,1]]},"references-count":22,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae018","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1,1]]},"published":{"date-parts":[[2024,1,1]]},"article-number":"btae018"}}