{"doi":"10.1093/bioinformatics/bty560","title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","abstract":"<h4>Motivation</h4>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.<h4>Results</h4>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 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools.<h4>Availability and implementation</h4>The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.","journal":"Bioinformatics","year":2018,"id":1962,"datarank":15.056237422880962,"base_score":10.25923706839836,"endowment":10.25923706839836,"self_citation_contribution":1.5388855602597542,"citation_network_contribution":13.517351862621208,"self_endowment_contribution":1.5388855602597542,"citer_contribution":13.517351862621208,"corpus_percentile":98.1,"corpus_rank":177,"citation_count":28544,"citer_count":199,"citers_with_citation_signal":199,"citers_with_endowment":199,"datacite_reuse_total":0,"is_dataset":false,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-09-01","authors":[{"id":22240,"name":"Yanqing Zhou","orcid":"0000-0002-9319-2579","position":1,"is_corresponding":false},{"id":22241,"name":"Yaru Chen","orcid":"0000-0003-2549-8880","position":2,"is_corresponding":false},{"id":22242,"name":"Jia Gu","orcid":"0000-0001-7498-9892","position":3,"is_corresponding":false},{"id":22239,"name":"Shifu Chen","orcid":"0000-0001-5799-653X","position":0,"is_corresponding":true}],"reference_count":16,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}