{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:35:00Z","timestamp":1772138100116,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,11,6]],"date-time":"2019-11-06T00:00:00Z","timestamp":1572998400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/M009122\/1"],"award-info":[{"award-number":["BB\/M009122\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["MR\/L015080\/1"],"award-info":[{"award-number":["MR\/L015080\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015846","name":"Welsh Government","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100015846","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Genomics Partnership Wales"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Influenza viruses represent a global public health burden due to annual epidemics and pandemic potential. Due to a rapidly evolving RNA genome, inter-species transmission, intra-host variation, and noise in short-read data, reads can be lost during mapping, and de novo assembly can be time consuming and result in misassembly. We assessed read loss during mapping and designed a graph-based classifier, VAPOR, for selecting mapping references, assembly validation and detection of strains of non-human origin.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Standard human reference viruses were insufficient for mapping diverse influenza samples in simulation. VAPOR retrieved references for 257 real whole-genome sequencing samples with a mean of &amp;gt;99.8% identity to assemblies, and increased the proportion of mapped reads by up to 13.3% compared to standard references. VAPOR has the potential to improve the robustness of bioinformatics pipelines for surveillance and could be adapted to other RNA viruses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>VAPOR is available at https:\/\/github.com\/connor-lab\/vapor.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz814","type":"journal-article","created":{"date-parts":[[2019,10,30]],"date-time":"2019-10-30T16:12:10Z","timestamp":1572451930000},"page":"1681-1688","source":"Crossref","is-referenced-by-count":7,"title":["Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications"],"prefix":"10.1093","volume":"36","author":[{"given":"Joel A","family":"Southgate","sequence":"first","affiliation":[{"name":"Organisms and Environment Division, School of Biosciences, Cardiff University , Cardiff CF10 3AX, UK"}]},{"given":"Matthew J","family":"Bull","sequence":"additional","affiliation":[{"name":"Organisms and Environment Division, School of Biosciences, Cardiff University , Cardiff CF10 3AX, UK"},{"name":"Public Health Wales, University Hospital of Wales , Cardiff CF14 4XW, UK"}]},{"given":"Clare M","family":"Brown","sequence":"additional","affiliation":[{"name":"Organisms and Environment Division, School of Biosciences, Cardiff University , Cardiff CF10 3AX, UK"}]},{"given":"Joanne","family":"Watkins","sequence":"additional","affiliation":[{"name":"Public Health Wales, University Hospital of Wales , Cardiff CF14 4XW, UK"}]},{"given":"Sally","family":"Corden","sequence":"additional","affiliation":[{"name":"Public Health Wales, University Hospital of Wales , Cardiff CF14 4XW, UK"}]},{"given":"Benjamin","family":"Southgate","sequence":"additional","affiliation":[{"name":"MRC Centre for Regenerative Medicine, University of Edinburgh , Edinburgh EH16 4UU, UK"}]},{"given":"Catherine","family":"Moore","sequence":"additional","affiliation":[{"name":"Public Health Wales, University Hospital of Wales , Cardiff CF14 4XW, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2394-6504","authenticated-orcid":false,"given":"Thomas R","family":"Connor","sequence":"additional","affiliation":[{"name":"Organisms and Environment Division, School of Biosciences, Cardiff University , Cardiff CF10 3AX, UK"},{"name":"Public Health Wales, University Hospital of Wales , Cardiff CF14 4XW, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,11,6]]},"reference":[{"key":"2023060911575792700_btz814-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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