{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T07:14:10Z","timestamp":1765610050554,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T00:00:00Z","timestamp":1597017600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008902","name":"Los Alamos National Laboratory","doi-asserted-by":"publisher","award":["20200732ER"],"award-info":[{"award-number":["20200732ER"]}],"id":[{"id":"10.13039\/100008902","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000774","name":"Defense Threat Reduction Agency","doi-asserted-by":"publisher","award":["CB10152","CB10623"],"award-info":[{"award-number":["CB10152","CB10623"]}],"id":[{"id":"10.13039\/100000774","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Energy Office of Science","award":["KP160101"],"award-info":[{"award-number":["KP160101"]}]},{"name":"National Virtual Biotechnology Laboratory"},{"name":"Department of Energy national laboratories focused on response to COVID-19"},{"name":"Coronavirus CARES Act"},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-0735191","DBI-1265383","DBI-1743442"],"award-info":[{"award-number":["DBI-0735191","DBI-1265383","DBI-1743442"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Polymerase chain reaction-based assays are the current gold standard for detecting and diagnosing SARS-CoV-2. However, as SARS-CoV-2 mutates, we need to constantly assess whether existing PCR-based assays will continue to detect all known viral strains. To enable the continuous monitoring of SARS-CoV-2 assays, we have developed a web-based assay validation algorithm that checks existing PCR-based assays against the ever-expanding genome databases for SARS-CoV-2 using both thermodynamic and edit-distance metrics. The assay-screening results are displayed as a heatmap, showing the number of mismatches between each detection and each SARS-CoV-2 genome sequence. Using a mismatch threshold to define detection failure, assay performance is summarized with the true-positive rate (recall) to simplify assay comparisons.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The assay evaluation website and supporting software are Open Source and freely available at https:\/\/covid19.edgebioinformatics.org\/#\/assayValidation, https:\/\/github.com\/jgans\/thermonucleotide BLAST and https:\/\/github.com\/LANL-Bioinformatics\/assay_validation.<\/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               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