{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,9]],"date-time":"2024-09-09T04:43:36Z","timestamp":1725857016473},"publisher-location":"Cham","reference-count":25,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319401256"},{"type":"electronic","value":"9783319401263"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-3-319-40126-3_15","type":"book-chapter","created":{"date-parts":[[2016,5,31]],"date-time":"2016-05-31T07:50:23Z","timestamp":1464681023000},"page":"141-149","source":"Crossref","is-referenced-by-count":0,"title":["RUbioSeq+: An Application that Executes Parallelized Pipelines to Analyse Next-Generation Sequencing Data"],"prefix":"10.1007","author":[{"given":"Miriam","family":"Rubio-Camarillo","sequence":"first","affiliation":[]},{"given":"Hugo","family":"L\u00f3pez-Fern\u00e1ndez","sequence":"additional","affiliation":[]},{"given":"Gonzalo","family":"G\u00f3mez-L\u00f3pez","sequence":"additional","affiliation":[]},{"given":"\u00c1ngel","family":"Carro","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 Mar\u00eda","family":"Fern\u00e1ndez","sequence":"additional","affiliation":[]},{"given":"Florentino","family":"Fdez-Riverola","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Glez-Pe\u00f1a","sequence":"additional","affiliation":[]},{"given":"David G.","family":"Pisano","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,6,1]]},"reference":[{"issue":"5","key":"15_CR1","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nbt0509-455","volume":"27","author":"C Trapnell","year":"2009","unstructured":"Trapnell, C., Salzberg, S.L.: How to map billions of short reads onto genomes. Nat. Biotech. 27(5), 455\u2013457 (2009)","journal-title":"Nat. Biotech."},{"issue":"8","key":"15_CR2","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/nrg3767","volume":"15","author":"L Ding","year":"2014","unstructured":"Ding, L., Wendl, M.C., McMichael, J.F., Raphael, B.J.: Expanding the computational toolbox for mining cancer genomes. Nat. Rev. Genet. 15(8), 556\u2013570 (2014)","journal-title":"Nat. Rev. Genet."},{"issue":"3","key":"15_CR3","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1038\/nbt.2134","volume":"30","author":"HY Lam","year":"2012","unstructured":"Lam, H.Y., Pan, C., Clark, M.J., Lacroute, P., Chen, R., Haraksingh, R., O\u2019Huallachain, M., Gerstein, M.B., Kidd, J.M., Bustamante, C.D., Snyder, M.: Detecting and annotating genetic variations using the HugeSeq pipeline. Nat. Biotechnol. 30(3), 226\u2013229 (2012)","journal-title":"Nat. Biotechnol."},{"unstructured":"bcbio toolkit. https:\/\/bcbio-nextgen.readthedocs.org","key":"15_CR4"},{"unstructured":"Omics Pipe. https:\/\/bitbucket.org\/sulab\/omics_pipe","key":"15_CR5"},{"issue":"8","key":"15_CR6","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","volume":"11","author":"J Goecks","year":"2010","unstructured":"Goecks, J., Nekrutenko, A., Taylor, J., The Galaxy Team: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11(8), R86 (2010)","journal-title":"Genome Biol."},{"issue":"1","key":"15_CR7","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.1809","volume":"9","author":"F Halbritter","year":"2011","unstructured":"Halbritter, F., Vaidya, H.J., Tomlinson, S.R.: GeneProf: analysis of high-throughput sequencing experiments. Nat. Methods 9(1), 7\u20138 (2011)","journal-title":"Nat. Methods"},{"issue":"11","key":"15_CR8","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/nbt.1505","volume":"26","author":"H Ji","year":"2008","unstructured":"Ji, H., Jiang, H., Ma, W., Johnson, D.S., Myers, R.M., Wong, W.H.: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat. Biotechnol. 26(11), 1293\u20131300 (2008)","journal-title":"Nat. Biotechnol."},{"issue":"13","key":"15_CR9","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1093\/bioinformatics\/btt203","volume":"29","author":"M Rubio-Camarillo","year":"2013","unstructured":"Rubio-Camarillo, M., G\u00f3mez-L\u00f3pez, G., Fern\u00e1ndez, J.M., Valencia, A., Pisano, D.G.: RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses. Bioinformatics 29(13), 1687\u20131689 (2013)","journal-title":"Bioinformatics"},{"key":"15_CR10","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W., Liu, X.S.: Model-based Analysis of ChIP-Seq (MACS). Genome Biology 9, R137 (2008)","journal-title":"Genome Biology"},{"issue":"9","key":"15_CR11","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1093\/bioinformatics\/btq128","volume":"26","author":"H Xu","year":"2010","unstructured":"Xu, H., Handoko, L., Wei, X., Ye, C., Sheng, J., Wei, C.L., Lin, F., Sung, W.K.: A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 26(9), 1199\u20131204 (2010)","journal-title":"Bioinformatics"},{"unstructured":"FastQC project. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/","key":"15_CR12"},{"issue":"14","key":"15_CR13","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754\u20131760 (2009)","journal-title":"Bioinformatics"},{"unstructured":"Picard tools. http:\/\/broadinstitute.github.io\/picard\/","key":"15_CR14"},{"key":"15_CR15","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., 1000 Genome Project Data Processing Subgroup: The Sequence alignment\/map (SAM) format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009)","journal-title":"Bioinformatics"},{"key":"15_CR16","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1214\/11-AOAS466","volume":"5","author":"Q Li","year":"2011","unstructured":"Li, Q., Brown, J., Huang, H., Bickel, P.: Measuring reproducibility of high-throughput experiments. Ann. Appl. Stat. 5, 1752\u20131779 (2011)","journal-title":"Ann. Appl. Stat."},{"key":"15_CR17","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1186\/1471-2105-11-415","volume":"11","author":"M Salmon-Divon","year":"2010","unstructured":"Salmon-Divon, M., Dvinge, H., Tammoja, K., Bertone, P.: PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci. BMC Bioinformatics 11, 415 (2010)","journal-title":"BMC Bioinformatics"},{"issue":"11","key":"15_CR18","doi-asserted-by":"crossref","first-page":"e7767","DOI":"10.1371\/journal.pone.0007767","volume":"4","author":"N Homer","year":"2009","unstructured":"Homer, N., Merriman, B., Nelson, S.F.: BFAST: an alignment tool for large scale genome resequencing. PLoS One 4(11), e7767 (2009)","journal-title":"PLoS One"},{"key":"15_CR19","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"M DePristo","year":"2011","unstructured":"DePristo, M., Banks, E., Poplin, R., Garimella, K., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M.A., Hanna, M., McKenna, A., Fennell, T., Kernytsky, A., Sivachenko, A., Cibulskis, K., Gabriel, S., Altshuler, D., Daly, M.: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43, 491\u2013498 (2011)","journal-title":"Nature Genetics"},{"key":"15_CR20","first-page":"11.10.1","volume":"43","author":"GA Auwera Van der","year":"2013","unstructured":"Van der Auwera, G.A., Carneiro, M., Hartl, C., Poplin, R., del Angel, G., Levy-Moonshine, A., Jordan, T., Shakir, K., Roazen, D., Thibault, J., Banks, E., Garimella, K., Altshuler, D., Gabriel, S., DePristo, M.: From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Current Protocols in Bioinformatics 43, 11.10.1\u201311.10.33 (2013)","journal-title":"Current Protocols in Bioinformatics"},{"issue":"16","key":"15_CR21","doi-asserted-by":"crossref","first-page":"2069","DOI":"10.1093\/bioinformatics\/btq330","volume":"26","author":"W McLaren","year":"2010","unstructured":"McLaren, W., Pritchard, P., Rios, D., Chen, Y., Flicek, P., Cunningham, F.: Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26(16), 2069\u20132070 (2010)","journal-title":"Bioinformatics"},{"issue":"10","key":"15_CR22","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/bioinformatics\/bts146","volume":"28","author":"J Li","year":"2012","unstructured":"Li, J., Lupat, R., Amarasinghe, K.C., Thompson, E.R., Doyle, M.A., Ryland, G.L., Tothill, R.W., Halgamuge, S.K., Campbell, I.G., Gorringe, K.L.: CONTRA: copy number analysis for targeted resequencing. Bioinformatics 28(10), 1307\u20131313 (2012)","journal-title":"Bioinformatics"},{"issue":"11","key":"15_CR23","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","volume":"27","author":"F Krueger","year":"2011","unstructured":"Krueger, F., Andrews, S.R.: Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27(11), 1571\u20131572 (2011)","journal-title":"Bioinformatics"},{"issue":"13","key":"15_CR24","doi-asserted-by":"crossref","first-page":"2034","DOI":"10.1182\/blood-2013-05-504308","volume":"123","author":"JP Vaqu\u00e9","year":"2014","unstructured":"Vaqu\u00e9, J.P., G\u00f3mez-L\u00f3pez, G., Mons\u00e1lvez, V., Varela, I., Mart\u00ednez, N., P\u00e9rez, C., Dom\u00ednguez, O., Gra\u00f1a, O., et al.: PLCG1 mutations in cutaneous T-cell lymphomas. Blood 123(13), 2034\u20132043 (2014)","journal-title":"Blood"},{"doi-asserted-by":"crossref","unstructured":"Cuadrado, A., Remeseiro, S., Gra\u00f1a, O., Pisano, D.G., Losada, A.: The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues. Nucleic Acids Res., March 3, 2015. doi: 10.1093\/nar\/gkv144","key":"15_CR25","DOI":"10.1093\/nar\/gkv144"}],"container-title":["Advances in Intelligent Systems and Computing","10th International Conference on Practical Applications of Computational Biology & Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-40126-3_15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,24]],"date-time":"2017-06-24T15:23:06Z","timestamp":1498317786000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-40126-3_15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9783319401256","9783319401263"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-40126-3_15","relation":{},"ISSN":["2194-5357","2194-5365"],"issn-type":[{"type":"print","value":"2194-5357"},{"type":"electronic","value":"2194-5365"}],"subject":[],"published":{"date-parts":[[2016]]}}}