{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T14:49:42Z","timestamp":1742914182511,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":22,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642288388"},{"type":"electronic","value":"9783642288395"}],"license":[{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012]]},"DOI":"10.1007\/978-3-642-28839-5_23","type":"book-chapter","created":{"date-parts":[[2012,3,5]],"date-time":"2012-03-05T22:33:40Z","timestamp":1330986820000},"page":"197-207","source":"Crossref","is-referenced-by-count":3,"title":["Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment"],"prefix":"10.1007","author":[{"given":"N.","family":"Medina-Medina","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A.","family":"Broka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Lacey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H.","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E. S.","family":"Klings","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C. T.","family":"Baldwin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. H.","family":"Steinberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P.","family":"Sebastiani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"23_CR1","doi-asserted-by":"crossref","unstructured":"Craig Venter, J., et al.: The sequence of the human genome. Science\u00a0291(5507), 1304\u20131351 (2001); doi:10.1126\/science.1058040","DOI":"10.1126\/science.291.5507.1155d"},{"issue":"4","key":"23_CR2","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1016\/0888-7543(89)90142-0","volume":"5","author":"R.L. Sinsheimer","year":"1989","unstructured":"Sinsheimer, R.L.: Sequencing the human genome: summary report of the Santa Fe workshop. Genomics\u00a05(4), 954\u2013956 (1989)","journal-title":"Genomics"},{"key":"23_CR3","unstructured":"US Department of Health and Human Services and Department of Energy: Understanding our genetic inheritance. The U.S. human genome project: the first five years. US Dept. of Health and Human Services, Washington, DC (1990)"},{"issue":"1","key":"23_CR4","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1016\/0003-2697(86)90536-1","volume":"154","author":"E.C. Strauss","year":"1986","unstructured":"Strauss, E.C., Kobori, J.A., Siu, G., Hood, L.E.: Specific-primer-directed DNA sequencing. Anal. Biochem.\u00a0154(1), 353\u2013360 (1986)","journal-title":"Anal. Biochem."},{"key":"23_CR5","unstructured":"Yang, G., Ho, M.-H., Hubbell, E.: High-throughput microarray-based genotyping. In: IEEE Computational Systems Bioinformatics Conference, pp. 586\u2013587 (2004)"},{"issue":"9","key":"23_CR6","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1242\/jeb.001370","volume":"210","author":"N. Hall","year":"2007","unstructured":"Hall, N.: Advanced sequencing technologies and their wider impact in microbiology. The Journal of Experimental Biology\u00a0210(9), 1518\u20131525 (2007); doi:10.1242\/jeb.001370","journal-title":"The Journal of Experimental Biology"},{"key":"23_CR7","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1109\/MC.2002.1016901","volume":"35","author":"M. Pop","year":"2002","unstructured":"Pop, M., Salzberg, S., Shumway, M.: Genome sequence assembly: algorithms and issues. IEEE Computer\u00a035, 47\u201354 (2002)","journal-title":"IEEE Computer"},{"key":"23_CR8","unstructured":"Mount, D.M.: Bioinformatics: sequence and genome analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor,(2004); ISBN: 0-87969-608-7"},{"issue":"3","key":"23_CR9","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","volume":"48","author":"S.B. Needleman","year":"1970","unstructured":"Needleman, S.B., Wunsch, C.D.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology\u00a048(3), 443\u2013453 (1970)","journal-title":"Journal of Molecular Biology"},{"issue":"1","key":"23_CR10","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/0022-2836(81)90087-5","volume":"147","author":"T.F. Smith","year":"1981","unstructured":"Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. Journal of Molecular Biology\u00a0147(1), 195\u2013197 (1981)","journal-title":"Journal of Molecular Biology"},{"key":"23_CR11","unstructured":"Drummond, A.J., Ashton, B., Buxton, S., Cheung, M., Cooper, A., Heled, J., Kearse, M., Moir, R., Stones-Havas, S., Sturrock, S., Thierer, T., Wilson, A.: Geneious v5.1 (2010), \n                    http:\/\/www.geneious.com"},{"key":"23_CR12","unstructured":"CLC Main Workbench: A comprehensive workbench for advanced DNA, RNA, and protein analyses, \n                    http:\/\/www.clcbio.com"},{"key":"23_CR13","doi-asserted-by":"crossref","unstructured":"Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology\u00a010(3), R25 (2009)","DOI":"10.1186\/gb-2009-10-3-r25"},{"issue":"19","key":"23_CR14","doi-asserted-by":"publisher","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\u00a025(19), 1754\u20131760 (2009)","journal-title":"Bioinformatics"},{"issue":"10","key":"23_CR15","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1101\/gr.4086505","volume":"15","author":"B. Giardine","year":"2005","unstructured":"Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Miller, W., et al.: Galaxy: a platform for interactive large-scale genome analysis. Genome Research\u00a015(10), 1451\u20131455 (2005)","journal-title":"Genome Research"},{"key":"23_CR16","unstructured":"Illumina: Illumina sequencing, \n                    http:\/\/www.illumina.com"},{"issue":"9","key":"23_CR17","first-page":"46","volume":"21","author":"M. Nelson","year":"1996","unstructured":"Nelson, M.: Data compression with the Burrows-Wheeler transform. Dr. Dobb\u2019s Journal of Software Tools\u00a021(9), 46\u201350 (1996)","journal-title":"Dr. Dobb\u2019s Journal of Software Tools"},{"issue":"16","key":"23_CR18","doi-asserted-by":"publisher","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 format and SAMtools. Bioinformatics\u00a025(16), 2078\u20132079 (2009)","journal-title":"Bioinformatics"},{"issue":"14","key":"23_CR19","doi-asserted-by":"publisher","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\u00a025(14), 1754\u20131760 (2009)","journal-title":"Bioinformatics"},{"key":"23_CR20","doi-asserted-by":"crossref","unstructured":"Hoffmann, S., Otto, C., Kurtz, S., Sharma, C.M., Khaitovich, P., Vogel, J., Stadler, P.F., Hackermuller, J.: Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Computational Biology\u00a05(9), R1000502 (2009)","DOI":"10.1371\/journal.pcbi.1000502"},{"issue":"20","key":"23_CR21","doi-asserted-by":"publisher","first-page":"2790","DOI":"10.1093\/bioinformatics\/btr477","volume":"27","author":"M. Ruffalo","year":"2011","unstructured":"Ruffalo, M., Laframboise, T., Koyut\u00fcrk, M.: Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics\u00a027(20), 2790\u20132796 (2011)","journal-title":"Bioinformatics"},{"issue":"5","key":"23_CR22","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1093\/bib\/bbq015","volume":"11","author":"L. Heng","year":"2010","unstructured":"Heng, L., Nils, H.: A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics\u00a011(5), 473\u2013483 (2010)","journal-title":"Briefings in Bioinformatics"}],"container-title":["Advances in Intelligent and Soft Computing","6th International Conference on Practical Applications of Computational Biology & Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-28839-5_23","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,18]],"date-time":"2023-01-18T18:09:17Z","timestamp":1674065357000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-642-28839-5_23"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012]]},"ISBN":["9783642288388","9783642288395"],"references-count":22,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-28839-5_23","relation":{},"ISSN":["1867-5662","1867-5670"],"issn-type":[{"type":"print","value":"1867-5662"},{"type":"electronic","value":"1867-5670"}],"subject":[],"published":{"date-parts":[[2012]]}}}