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Most adapter trimming tools require adapter information as input. However, adapter information is hard to access, specified incorrectly, or not provided with publicly available datasets, hampering their reproducibility and reusability. Manual identification of adapter patterns from raw reads is labor-intensive and error-prone. Moreover, the use of randomized adapters to reduce ligation biases during library preparation makes adapter detection even more challenging. Here, we present FindAdapt, a Python package for fast and accurate detection of adapter patterns without relying on prior information. We demonstrated that FindAdapt was far superior to existing approaches. It identified adapters successfully in 180 simulation datasets with diverse read structures and 3,184 real datasets covering a variety of commercial and customized small RNA library preparation kits. FindAdapt is stand-alone software that can be easily integrated into small RNA sequencing analysis pipelines.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1011786","type":"journal-article","created":{"date-parts":[[2024,1,22]],"date-time":"2024-01-22T18:31:33Z","timestamp":1705948293000},"page":"e1011786","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":7,"title":["FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing"],"prefix":"10.1371","volume":"20","author":[{"given":"Hua-Chang","family":"Chen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Shyr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8892-7078","authenticated-orcid":true,"given":"Qi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2024,1,22]]},"reference":[{"issue":"6","key":"pcbi.1011786.ref001","article-title":"Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis","volume":"11","author":"S Benesova","year":"2021","journal-title":"Diagnostics (Basel)"},{"issue":"4","key":"pcbi.1011786.ref002","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/s41556-022-00880-5","article-title":"Exploring the expanding universe of small RNAs","volume":"24","author":"J Shi","year":"2022","journal-title":"Nat Cell Biol"},{"issue":"11","key":"pcbi.1011786.ref003","doi-asserted-by":"crossref","first-page":"1788","DOI":"10.1016\/j.neuron.2022.03.008","article-title":"Astrocytes and oligodendrocytes undergo subtype-specific transcriptional changes in Alzheimer\u2019s disease","volume":"110","author":"JS Sadick","year":"2022","journal-title":"Neuron"},{"key":"pcbi.1011786.ref004","doi-asserted-by":"crossref","first-page":"921868","DOI":"10.3389\/fvets.2022.921868","article-title":"Expression characteristics of piRNAs in ovine luteal phase and follicular phase ovaries","volume":"9","author":"C Li","year":"2022","journal-title":"Front Vet Sci"},{"key":"pcbi.1011786.ref005","doi-asserted-by":"crossref","first-page":"799733","DOI":"10.3389\/fimmu.2022.799733","article-title":"Changes in the Small Noncoding RNAome During M1 and M2 Macrophage Polarization","volume":"13","author":"D Ma","year":"2022","journal-title":"Front Immunol"},{"issue":"7","key":"pcbi.1011786.ref006","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1136\/jmedgenet-2021-108327","article-title":"Disorders and roles of tsRNA, snoRNA, snRNA and piRNA in cancer","volume":"59","author":"L Xiao","year":"2022","journal-title":"J Med Genet"},{"issue":"20","key":"pcbi.1011786.ref007","doi-asserted-by":"crossref","first-page":"31974","DOI":"10.1364\/OE.436293","article-title":"Cause-aware failure detection using an interpretable XGBoost for optical networks","volume":"29","author":"C Zhang","year":"2021","journal-title":"Opt Express"},{"issue":"1","key":"pcbi.1011786.ref008","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s12967-020-02298-9","article-title":"Optimization of small RNA library preparation protocol from human urinary exosomes","volume":"18","author":"D Olivares","year":"2020","journal-title":"J Transl Med"},{"key":"pcbi.1011786.ref009","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1007\/978-1-4939-9042-9_4","article-title":"Bioinformatic Analysis of Small RNA Sequencing Libraries","volume":"1932","author":"RA Chavez Montes","year":"2019","journal-title":"Methods Mol Biol"},{"issue":"1","key":"pcbi.1011786.ref010","doi-asserted-by":"crossref","first-page":"3","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M. Martin","year":"2011","journal-title":"EMBnet journal"},{"key":"pcbi.1011786.ref011","unstructured":"Hannon. 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