{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T08:51:39Z","timestamp":1780563099734,"version":"3.54.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2018,9,9]],"date-time":"2018-09-09T00:00:00Z","timestamp":1536451200000},"content-version":"vor","delay-in-days":8,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Special Funds for Future Industries of Shenzhen","award":["JSGG20160229123927512"],"award-info":[{"award-number":["JSGG20160229123927512"]}]},{"DOI":"10.13039\/501100001809","name":"National Science Foundation of China","doi-asserted-by":"publisher","award":["61472411"],"award-info":[{"award-number":["61472411"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I\/O inefficient.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2\u20135 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The open-source code and corresponding instructions are available at https:\/\/github.com\/OpenGene\/fastp.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty560","type":"journal-article","created":{"date-parts":[[2018,7,7]],"date-time":"2018-07-07T01:42:12Z","timestamp":1530927732000},"page":"i884-i890","source":"Crossref","is-referenced-by-count":26166,"title":["fastp: an ultra-fast all-in-one FASTQ preprocessor"],"prefix":"10.1093","volume":"34","author":[{"given":"Shifu","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China"},{"name":"Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanqing","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaru","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, HaploX Biotechnology, Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Gu","sequence":"additional","affiliation":[{"name":"Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,9,8]]},"reference":[{"key":"2023061313520485800_bty560-B1","unstructured":"Andrews\n       \u00a0S.\n           (2010) \nA quality control tool for high throughput sequence data. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"2023061313520485800_bty560-B2","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1001\/jama.2015.7120","article-title":"Noninvasive prenatal testing and incidental detection of occult maternal malignancies","volume":"314","author":"Bianchi","year":"2015","journal-title":"JAMA"},{"key":"2023061313520485800_bty560-B3","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":"2023061313520485800_bty560-B4","unstructured":"Brad Chapman\n       \u00a0R.K.\n      \u00a0et al. (2018) Validated, Scalable, Community Developed Variant Calling, RNA-Seq and Small RNA Analysis, https:\/\/github.com\/chapmanb\/bcbio-nextgen."},{"key":"2023061313520485800_bty560-B5","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s12859-017-1469-3","article-title":"AfterQC: automatic filtering, trimming, error removing and quality control for fastq data","volume":"18","author":"Chen","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2023061313520485800_bty560-B6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/gix120","article-title":"SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data","volume":"7","author":"Chen","year":"2018","journal-title":"Gigascience"},{"key":"2023061313520485800_bty560-B7","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1038\/nmeth.3505","article-title":"SpeedSeq: ultra-fast personal genome analysis and interpretation","volume":"12","author":"Chiang","year":"2015","journal-title":"Nat. Methods"},{"key":"2023061313520485800_bty560-B8","doi-asserted-by":"crossref","DOI":"10.1007\/s11912-017-0564-y","article-title":"The emerging role of \u201cLiquid Biopsies,\u201d circulating tumor cells, and circulating cell-free tumor dna in lung cancer diagnosis and identification of resistance mutations","volume":"19","author":"Esposito","year":"2017","journal-title":"Curr. Oncol. Rep."},{"key":"2023061313520485800_bty560-B9","doi-asserted-by":"crossref","first-page":"2586","DOI":"10.1038\/nprot.2014.170","article-title":"Detecting ultralow-frequency mutations by duplex sequencing","volume":"9","author":"Kennedy","year":"2014","journal-title":"Nat. Protoc."},{"key":"2023061313520485800_bty560-B10","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023061313520485800_bty560-B11","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061313520485800_bty560-B12","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023061313520485800_bty560-B13","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":"2023061313520485800_bty560-B14","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1038\/nbt.3520","article-title":"Integrated digital error suppression for improved detection of circulating tumor DNA","volume":"34","author":"Newman","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2023061313520485800_bty560-B15","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy","volume":"27","author":"Smith","year":"2017","journal-title":"Genome Res."},{"key":"2023061313520485800_bty560-B16","unstructured":"Valentine Svensson\n       \u00a0R.K.\n      \u00a0et al. (2018) Tools for Processing UMI RNA-Tag Data, https:\/\/github.com\/vals\/umis."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/i884\/50582648\/bioinformatics_34_17_i884.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/17\/i884\/50582648\/bioinformatics_34_17_i884.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T09:54:49Z","timestamp":1686650089000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/17\/i884\/5093234"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,9,1]]},"references-count":16,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2018,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty560","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/274100","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,1]]},"published":{"date-parts":[[2018,9,1]]}}}