{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T14:34:35Z","timestamp":1772289275632,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,26]],"date-time":"2017-10-26T00:00:00Z","timestamp":1508976000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20150681"],"award-info":[{"award-number":["BK20150681"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["71704081"],"award-info":[{"award-number":["71704081"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>High throughput bisulfite sequencing (BS-seq) is an important technology to generate single-base DNA methylomes in both plants and animals. In order to accelerate the data analysis of BS-seq data, toolkits for visualization are required.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>ViewBS, an open-source toolkit, can extract and visualize the DNA methylome data easily and with flexibility. By using Tabix, ViewBS can visualize BS-seq for large datasets quickly. ViewBS can generate publication-quality figures, such as meta-plots, heat maps and violin-boxplots, which can help users to answer biological questions. We illustrate its application using BS-seq data from Arabidopsis thaliana.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability<\/jats:title><jats:p>ViewBS is freely available at: https:\/\/github.com\/xie186\/ViewBS.<\/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\/btx633","type":"journal-article","created":{"date-parts":[[2017,10,25]],"date-time":"2017-10-25T19:22:29Z","timestamp":1508959349000},"page":"708-709","source":"Crossref","is-referenced-by-count":77,"title":["ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data"],"prefix":"10.1093","volume":"34","author":[{"given":"Xiaosan","family":"Huang","sequence":"first","affiliation":[{"name":"College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No.6 Tongwei Road Nanjing, P. R. China"}]},{"given":"Shaoling","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No.6 Tongwei Road Nanjing, P. R. China"}]},{"given":"Kongqing","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Rural Development, Nanjing Agricultural University, No.6 Tongwei Road Nanjing, P. R. China"}]},{"given":"Jyothi","family":"Thimmapuram","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, Purdue University, 155 South Grant Street, West Lafayette, Indiana, USA"}]},{"given":"Shaojun","family":"Xie","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, Purdue University, 155 South Grant Street, West Lafayette, Indiana, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,10,26]]},"reference":[{"key":"2023012712401587900_btx633-B1","doi-asserted-by":"crossref","first-page":"R87.","DOI":"10.1186\/gb-2012-13-10-r87","article-title":"methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles","volume":"13","author":"Akalin","year":"2012","journal-title":"Genome Biol"},{"key":"2023012712401587900_btx633-B2","doi-asserted-by":"crossref","first-page":"774.","DOI":"10.1186\/1471-2164-14-774","article-title":"BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data","volume":"14","author":"Guo","year":"2013","journal-title":"BMC Genomics"},{"key":"2023012712401587900_btx633-B3","doi-asserted-by":"crossref","first-page":"R83","DOI":"10.1186\/gb-2012-13-10-r83","article-title":"BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions","volume":"13","author":"Hansen","year":"2012","journal-title":"Genome Biol"},{"key":"2023012712401587900_btx633-B4","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1093\/bioinformatics\/bts264","article-title":"BRAT-BW: efficient and accurate mapping of bisulfite-treated reads","volume":"28","author":"Harris","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012712401587900_btx633-B5","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1080\/00031305.1998.10480559","article-title":"Violin plots: a box plot-density trace synergism","volume":"52","author":"Hintze","year":"1998","journal-title":"Am. 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