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Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https:\/\/bioinformatics.caf.ac.cn\/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package\/Docker\/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.<\/jats:p>","DOI":"10.1093\/bib\/bbz151","type":"journal-article","created":{"date-parts":[[2019,11,5]],"date-time":"2019-11-05T05:09:44Z","timestamp":1572930584000},"page":"463-473","source":"Crossref","is-referenced-by-count":40,"title":["Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing"],"prefix":"10.1093","volume":"22","author":[{"given":"Qi","family":"Liu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China"}]},{"given":"Changjun","family":"Ding","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China"}]},{"given":"Xiaoqiang","family":"Lang","sequence":"additional","affiliation":[{"name":"Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China"}]},{"given":"Ganggang","family":"Guo","sequence":"additional","affiliation":[{"name":"Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China 610041"}]},{"given":"Jiafei","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China"}]},{"given":"Xiaohua","family":"Su","sequence":"additional","affiliation":[{"name":"Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, 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