{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,6]],"date-time":"2026-04-06T19:04:06Z","timestamp":1775502246984,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2022,6,13]],"date-time":"2022-06-13T00:00:00Z","timestamp":1655078400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes for Health","doi-asserted-by":"crossref","award":["R01HL144599"],"award-info":[{"award-number":["R01HL144599"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes for Health","doi-asserted-by":"crossref","award":["T32HL007749"],"award-info":[{"award-number":["T32HL007749"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Kahn Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Here, we introduce SNIKT, a command-line tool for sequence-independent visual confirmation and input-assisted removal of adapter contamination in whole-genome shotgun or metagenomic shotgun long-read sequencing DNA or RNA data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>SNIKT is implemented in R and is compatible with Unix-like platforms. The source code, along with documentation, is freely available under an MIT license at https:\/\/github.com\/piyuranjan\/SNIKT.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac389","type":"journal-article","created":{"date-parts":[[2022,6,13]],"date-time":"2022-06-13T14:08:38Z","timestamp":1655129318000},"page":"3830-3832","source":"Crossref","is-referenced-by-count":7,"title":["SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data"],"prefix":"10.1093","volume":"38","author":[{"given":"Piyush","family":"Ranjan","sequence":"first","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA"}]},{"given":"Christopher A","family":"Brown","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA"},{"name":"Institute for Research on Innovation and Science, Institute for Social Research, University of Michigan , Ann Arbor, MI 48109, USA"}]},{"given":"John R","family":"Erb-Downward","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6875-4277","authenticated-orcid":false,"given":"Robert P","family":"Dickson","sequence":"additional","affiliation":[{"name":"Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School , Ann Arbor, MI 48109, USA"},{"name":"Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, MI 48109, USA"},{"name":"Weil Institute for Critical Care Research & Innovation , Ann Arbor, MI 48109, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,6,13]]},"reference":[{"key":"2023041405351355000_","author":"Baptiste","year":"2017","journal-title":"Package \u2018gridExtra\u2019 Miscellaneous Functions for \u201cGrid\u201d Graphics"},{"key":"2023041405351355000_","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":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bib\/bbx120","article-title":"A review of methods and databases for metagenomic classification and assembly","volume":"20","author":"Breitwieser","year":"2019","journal-title":"Brief. Bioinform"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: visualizing and processing long-read sequencing data","volume":"34","author":"De Coster","year":"2018","journal-title":"Bioinformatics"},{"key":"2023041405351355000_","author":"De Jonge","year":"2016","journal-title":"Docopt: Command-Line Interface Specification Language"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","DOI":"10.1128\/MRA.00299-21","article-title":"High-quality genome reconstruction of Candida albicans CHN1 using nanopore and illumina sequencing and hybrid assembly","volume":"10","author":"Garg","year":"2021","journal-title":"Microbiol. Resour. Announc"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v040.i03","article-title":"Dates and times made easy with lubridate","volume":"40","author":"Grolemund","year":"2011","journal-title":"J. Stat. Soft"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Gr\u00fcning","year":"2018","journal-title":"Nat. Methods"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu. Rev. Pathol"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s13059-016-1103-0","article-title":"The oxford nanopore MinION: delivery of nanopore sequencing to the genomics community","volume":"17","author":"Jain","year":"2016","journal-title":"Genome Biol"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J"},{"key":"2023041405351355000_","volume-title":"R: A language and environment for statistical ## computing","year":"2021"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"e59","DOI":"10.1002\/cpmb.59","article-title":"Overview of Next-Generation sequencing technologies","volume":"122","author":"Slatko","year":"2018","journal-title":"Curr. Protoc. Mol. Biol"},{"key":"2023041405351355000_","author":"Tange","year":"2018"},{"key":"2023041405351355000_","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"JOSS"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac389\/44152735\/btac389.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/15\/3830\/49884077\/btac389.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/15\/3830\/49884077\/btac389.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T01:39:16Z","timestamp":1700703556000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/15\/3830\/6607583"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,6,13]]},"references-count":15,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2022,8,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac389","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,8,1]]},"published":{"date-parts":[[2022,6,13]]}}}