{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T06:48:05Z","timestamp":1786603685222,"version":"3.56.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T00:00:00Z","timestamp":1669852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Health and Medical Research Council Investigator Grant","award":["1196832"],"award-info":[{"award-number":["1196832"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools either are not designed specifically for bacteriophages or are web- and email-based and require significant manual curation, which makes their integration into bioinformatic pipelines challenging. Pharokka was created to provide a tool that annotates bacteriophage genomes easily, rapidly and consistently with standards compliant outputs. Moreover, Pharokka requires only two lines of code to install and use and takes under 5\u2009min to run for an average 50-kb bacteriophage genome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Pharokka is implemented in Python and is available as a bioconda package using \u2018conda install -c bioconda pharokka\u2019. The source code is available on GitHub (https:\/\/github.com\/gbouras13\/pharokka). Pharokka has been tested on Linux-64 and MacOSX machines and on Windows using a Linux Virtual Machine.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac776","type":"journal-article","created":{"date-parts":[[2022,11,30]],"date-time":"2022-11-30T23:26:50Z","timestamp":1669850810000},"source":"Crossref","is-referenced-by-count":621,"title":["Pharokka: a fast scalable bacteriophage annotation tool"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5885-4186","authenticated-orcid":false,"given":"George","family":"Bouras","sequence":"first","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, SA 5070, Australia"},{"name":"Department of Surgery\u2014Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network , Adelaide, SA 5070, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5469-3397","authenticated-orcid":false,"given":"Roshan","family":"Nepal","sequence":"additional","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, SA 5070, Australia"},{"name":"Department of Surgery\u2014Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network , Adelaide, SA 5070, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6692-9478","authenticated-orcid":false,"given":"Ghais","family":"Houtak","sequence":"additional","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, SA 5070, Australia"},{"name":"Department of Surgery\u2014Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network , Adelaide, SA 5070, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alkis James","family":"Psaltis","sequence":"additional","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, SA 5070, Australia"},{"name":"Department of Surgery\u2014Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network , Adelaide, SA 5070, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter-John","family":"Wormald","sequence":"additional","affiliation":[{"name":"Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide , Adelaide, SA 5070, Australia"},{"name":"Department of Surgery\u2014Otolaryngology Head and Neck 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