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These analyses make use of 16S\/18S rRNA gene sequencing to identify taxa and predict species diversity. However, most available tools for analyzing microbiota data require adept programming skills and in-depth statistical knowledge for proper implementation. While long-read amplicon sequencing can lead to more accurate taxa predictions and is quickly becoming more common, practitioners have no easily accessible tools with which to perform their analyses.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present MOCHI, a GUI tool for microbiota amplicon sequencing analysis. MOCHI preprocesses sequences, assigns taxonomy, identifies different abundant species and predicts species diversity and function. It takes either taxonomic count table or FASTQ of partial 16S\/18S rRNA or full-length 16S rRNA gene as input. It performs analyses in real time and visualizes data in both tabular and graphical formats.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>MOCHI can be installed to run locally or accessed as a web tool at https:\/\/mochi.life.nctu.edu.tw.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac494","type":"journal-article","created":{"date-parts":[[2022,7,25]],"date-time":"2022-07-25T13:00:42Z","timestamp":1658754042000},"page":"4286-4292","source":"Crossref","is-referenced-by-count":10,"title":["MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis"],"prefix":"10.1093","volume":"38","author":[{"given":"Jun-Jie","family":"Zheng","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University , Hsinchu 30068, Taiwan"}]},{"given":"Po-Wen","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University , Hsinchu 30068, Taiwan"}]},{"given":"Tzu-Wen","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University , Taipei 11031, Taiwan"}]},{"given":"Yao-Jong","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Pediatrics and Institute of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University , Tainan 70428, Taiwan"}]},{"given":"Hua-Sheng","family":"Chiu","sequence":"additional","affiliation":[{"name":"Texas Children\u2019s Cancer Center, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"given":"Pavel","family":"Sumazin","sequence":"additional","affiliation":[{"name":"Texas Children\u2019s Cancer Center, Baylor College of Medicine , Houston, TX 77030, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4028-2375","authenticated-orcid":false,"given":"Ting-Wen","family":"Chen","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University , Hsinchu 30068, Taiwan"},{"name":"Department of Biological Science and Technology, National Yang Ming Chiao Tung University , Hsinchu 30068, Taiwan"},{"name":"Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University , Hsinchu 30068, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2022,7,25]]},"reference":[{"key":"2023041408241463100_","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1128\/mSystems.00191-16","article-title":"Deblur rapidly resolves single-nucleotide community sequence patterns","volume":"2","author":"Amir","year":"2017","journal-title":"mSystems"},{"key":"2023041408241463100_","author":"Anderson","year":"2005"},{"key":"2023041408241463100_","doi-asserted-by":"crossref","first-page":"2882","DOI":"10.1093\/bioinformatics\/btv287","article-title":"Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data","volume":"31","author":"A\u00dfhauer","year":"2015","journal-title":"Bioinformatics"},{"key":"2023041408241463100_","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13742-016-0111-z","article-title":"Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer","volume":"5","author":"Ben\u00edtez-P\u00e1ez","year":"2016","journal-title":"GigaSci"},{"key":"2023041408241463100_","first-page":"289","author":"Benjamini","year":"1995"},{"key":"2023041408241463100_","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. 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