{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,20]],"date-time":"2026-06-20T14:40:07Z","timestamp":1781966407599,"version":"3.54.5"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T00:00:00Z","timestamp":1683158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Genome Alberta and Genome Canada"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Proksee (https:\/\/proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes. Proksee accepts Illumina sequence reads as compressed FASTQ files or pre-assembled contigs in raw, FASTA, or GenBank format. Alternatively, users can supply a GenBank accession or a previously generated Proksee map in JSON format. Proksee then performs assembly (for raw sequence data), generates a graphical map, and provides an interface for customizing the map and launching further analysis jobs. Notable features of Proksee include unique and informative assembly metrics provided via a custom reference database of assemblies; a deeply integrated high-performance genome browser for viewing and comparing analysis results at individual base resolution (developed specifically for Proksee); an ever-growing list of embedded analysis tools whose results can be seamlessly added to the map or searched and explored in other formats; and the option to export graphical maps, analysis results, and log files for data sharing and research reproducibility. All these features are provided via a carefully designed multi-server cloud-based system that can easily scale to meet user demand and that ensures the web server is robust and responsive.<\/jats:p>","DOI":"10.1093\/nar\/gkad326","type":"journal-article","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T12:24:43Z","timestamp":1683203083000},"page":"W484-W492","source":"Crossref","is-referenced-by-count":1684,"title":["Proksee: in-depth characterization and visualization of bacterial genomes"],"prefix":"10.1093","volume":"51","author":[{"given":"Jason R","family":"Grant","sequence":"first","affiliation":[{"name":"Agriculture, Food & Nutritional Science, University of Alberta , Edmonton , Alberta \u00a0T6G 2P5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Enns","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg , Manitoba \u00a0R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Marinier","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg , Manitoba \u00a0R3E 3R2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnab","family":"Mandal","sequence":"additional","affiliation":[{"name":"Medical Microbiology & Infectious Diseases, University of Manitoba , Winnipeg , Manitoba \u00a0R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily K","family":"Herman","sequence":"additional","affiliation":[{"name":"Agriculture, Food & Nutritional Science, University of Alberta , Edmonton , Alberta \u00a0T6G 2P5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih-yu","family":"Chen","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg , Manitoba \u00a0R3E 3R2, Canada"},{"name":"Biochemistry & Medical Genetics, University of Manitoba , Winnipeg , Manitoba \u00a0R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morag","family":"Graham","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg , Manitoba \u00a0R3E 3R2, Canada"},{"name":"Medical Microbiology & Infectious Diseases, University of Manitoba , Winnipeg , Manitoba \u00a0R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1139-4458","authenticated-orcid":false,"given":"Gary","family":"Van\u00a0Domselaar","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory, Public Health Agency of Canada , Winnipeg , Manitoba \u00a0R3E 3R2, Canada"},{"name":"Medical Microbiology & Infectious Diseases, University of Manitoba , Winnipeg , Manitoba \u00a0R3E 0J9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4263-969X","authenticated-orcid":false,"given":"Paul","family":"Stothard","sequence":"additional","affiliation":[{"name":"Agriculture, Food & Nutritional Science, University of Alberta , Edmonton , Alberta \u00a0T6G 2P5, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,4]]},"reference":[{"key":"2023070504592856800_B1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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