{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,6]],"date-time":"2024-10-06T00:42:10Z","timestamp":1728175330627},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1575,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,15]]},"abstract":"Abstract<\/jats:title>\n Summary: Reduced representation bisulfite sequencing (RRBS) is a cost-effective approach for genome-wide methylation pattern profiling. Analyzing RRBS sequencing data is challenging and specialized alignment\/mapping programs are needed. Although such programs have been developed, a comprehensive solution that provides researchers with good quality and analyzable data is still lacking. To address this need, we have developed a Streamlined Analysis and Annotation Pipeline for RRBS data (SAAP-RRBS) that integrates read quality assessment\/clean-up, alignment, methylation data extraction, annotation, reporting and visualization. This package facilitates a rapid transition from sequencing reads to a fully annotated CpG methylation report to biological interpretation.<\/jats:p>\n Availability and implementation: SAAP-RRBS is freely available to non-commercial users at the web site http:\/\/ndc.mayo.edu\/mayo\/research\/biostat\/stand-alone-packages.cfm.<\/jats:p>\n Contact: \u00a0baheti.saurabh@mayo.edu or sun.zhifu@mayo.edu<\/jats:p>\n Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts337","type":"journal-article","created":{"date-parts":[[2012,6,12]],"date-time":"2012-06-12T02:28:09Z","timestamp":1339468089000},"page":"2180-2181","source":"Crossref","is-referenced-by-count":51,"title":["SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing"],"prefix":"10.1093","volume":"28","author":[{"given":"Zhifu","family":"Sun","sequence":"first","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Saurabh","family":"Baheti","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Sumit","family":"Middha","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Rahul","family":"Kanwar","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Yuji","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Xing","family":"Li","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Andreas S.","family":"Beutler","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Eric","family":"Klee","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Yan W.","family":"Asmann","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"E. Aubrey","family":"Thompson","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]},{"given":"Jean-Pierre A.","family":"Kocher","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, 2Department of Medical Oncology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA and 3Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, FL 32224, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,6,10]]},"reference":[{"key":"2023012512524378500_B1","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1038\/nbt.1681","article-title":"Quantitative comparison of genome-wide DNA methylation mapping technologies","volume":"28","author":"Bock","year":"2010","journal-title":"Nat. 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Biotechnol."},{"key":"2023012512524378500_B10","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1186\/1471-2105-10-232","article-title":"BSMAP: whole genome bisulfite sequence MAPping program","volume":"10","author":"Xi","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012512524378500_B11","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1093\/bioinformatics\/btr668","article-title":"RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing","volume":"28","author":"Xi","year":"2012","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2180\/48870146\/bioinformatics_28_16_2180.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/16\/2180\/48870146\/bioinformatics_28_16_2180.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:50:29Z","timestamp":1674669029000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/16\/2180\/324023"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,10]]},"references-count":11,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2012,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts337","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,8,15]]},"published":{"date-parts":[[2012,6,10]]}}}