{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T19:06:57Z","timestamp":1770491217638,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,3,11]],"date-time":"2020-03-11T00:00:00Z","timestamp":1583884800000},"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\/501100021177","name":"Shenzhen Bay Laboratory","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100021177","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Next-generation sequencing (NGS) data frequently suffer from poor-quality cycles and adapter contaminations therefore need to be preprocessed before downstream analyses. With the ever-growing throughput and read length of modern sequencers, the preprocessing step turns to be a bottleneck in data analysis due to unmet performance of current tools. Extra-fast and accurate adapter- and quality-trimming tools for sequencing data preprocessing are therefore still of urgent demand.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Ktrim was developed in this work. Key features of Ktrim include: built-in support to adapters of common library preparation kits; supports user-supplied, customized adapter sequences; supports both paired-end and single-end data; supports parallelization to accelerate the analysis. Ktrim was \u223c2\u201318 times faster than current tools and also showed high accuracy when applied on the testing datasets. Ktrim could thus serve as a valuable and efficient tool for short-read NGS data preprocessing.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source codes and scripts to reproduce the results descripted in this article are freely available at https:\/\/github.com\/hellosunking\/Ktrim\/, distributed under the GPL v3 license.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>sunkun@szbl.ac.cn<\/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\/btaa171","type":"journal-article","created":{"date-parts":[[2020,3,6]],"date-time":"2020-03-06T20:21:53Z","timestamp":1583526113000},"page":"3561-3562","source":"Crossref","is-referenced-by-count":51,"title":["Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data"],"prefix":"10.1093","volume":"36","author":[{"given":"Kun","family":"Sun","sequence":"first","affiliation":[{"name":"Shenzhen Bay Laboratory , Shenzhen 518055, China"}]}],"member":"286","published-online":{"date-parts":[[2020,3,11]]},"reference":[{"key":"2023062300082405500_btaa171-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":"2023062300082405500_btaa171-B2","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062300082405500_btaa171-B3","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1186\/1471-2105-15-182","article-title":"Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads","volume":"15","author":"Jiang","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023062300082405500_btaa171-B4","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":"2023062300082405500_btaa171-B5","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1186\/s12859-016-1069-7","article-title":"SeqPurge: highly-sensitive adapter trimming for paired-end NGS data","volume":"17","author":"Sturm","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2023062300082405500_btaa171-B6","first-page":"E5106","article-title":"Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing","volume":"115","author":"Sun","year":"2018","journal-title":"Proc. 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