{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T01:06:18Z","timestamp":1772931978853,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2019,12,16]],"date-time":"2019-12-16T00:00:00Z","timestamp":1576454400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Commonwealth Hill Trust and The Grains Research Development Corporation","award":["9175870"],"award-info":[{"award-number":["9175870"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>High throughput next generation sequencing (NGS) has become exceedingly cheap, facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and the outputs of popular bioinformatics tools such as FastQC and Picard can provide information on individual samples. Although these tools provide considerable power when carrying out QC, large sample numbers can make inspection of all samples and identification of systemic bias a challenge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present ngsReports, an R package designed for the management and visualization of NGS reports from within an R environment. The available methods allow direct import into R of FastQC reports along with outputs from other tools. Visualization can be carried out across many samples using default, highly customizable plots with options to perform hierarchical clustering to quickly identify outlier libraries. Moreover, these can be displayed in an interactive shiny app or HTML report for ease of analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The ngsReports package is available on Bioconductor and the GUI shiny app is available at https:\/\/github.com\/UofABioinformaticsHub\/shinyNgsreports.<\/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\/btz937","type":"journal-article","created":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T07:12:07Z","timestamp":1576134727000},"page":"2587-2588","source":"Crossref","is-referenced-by-count":102,"title":["ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files"],"prefix":"10.1093","volume":"36","author":[{"given":"Christopher M","family":"Ward","sequence":"first","affiliation":[{"name":"Department of Molecular and Biomedical Science"}]},{"given":"Thu-Hien","family":"To","sequence":"additional","affiliation":[{"name":"Bioinformatics Hub, School of Biological Sciences, University of Adelaide , Adelaide, SA 5005, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8197-3303","authenticated-orcid":false,"given":"Stephen M","family":"Pederson","sequence":"additional","affiliation":[{"name":"Bioinformatics Hub, School of Biological Sciences, University of Adelaide , Adelaide, SA 5005, Australia"}]}],"member":"286","published-online":{"date-parts":[[2019,12,16]]},"reference":[{"key":"2023013110260243600_btz937-B1","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2023013110260243600_btz937-B2","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013110260243600_btz937-B3","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013110260243600_btz937-B4","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"2023013110260243600_btz937-B6","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat. 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