{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T19:11:01Z","timestamp":1769368261966,"version":"3.49.0"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2010,3,15]],"date-time":"2010-03-15T00:00:00Z","timestamp":1268611200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"DOI":"10.1186\/1471-2105-11-130","type":"journal-article","created":{"date-parts":[[2010,3,16]],"date-time":"2010-03-16T07:15:45Z","timestamp":1268723745000},"source":"Crossref","is-referenced-by-count":35,"title":["Calling SNPs without a reference sequence"],"prefix":"10.1186","volume":"11","author":[{"given":"Aakrosh","family":"Ratan","sequence":"first","affiliation":[]},{"given":"Yu","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Vanessa M","family":"Hayes","sequence":"additional","affiliation":[]},{"given":"Stephan C","family":"Schuster","sequence":"additional","affiliation":[]},{"given":"Webb","family":"Miller","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,3,15]]},"reference":[{"key":"3587_CR1","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"D Zerbino","year":"2008","unstructured":"Zerbino D, Birney E: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 2008, 18: 821\u2013829. 10.1101\/gr.074492.107","journal-title":"Genome Research"},{"key":"3587_CR2","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1101\/gr.7337908","volume":"18","author":"J Butler","year":"2008","unstructured":"Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB: ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Research 2008, 18: 810\u2013820. 10.1101\/gr.7337908","journal-title":"Genome Research"},{"key":"3587_CR3","doi-asserted-by":"publisher","first-page":"e1000186","DOI":"10.1371\/journal.pcbi.1000186","volume":"4","author":"SL Salzberg","year":"2008","unstructured":"Salzberg SL, Sommer DD, Puiu D, Lee VT: Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Computational Biology 2008, 4: e1000186. 10.1371\/journal.pcbi.1000186","journal-title":"PLoS Computational Biology"},{"key":"3587_CR4","doi-asserted-by":"publisher","first-page":"1851","DOI":"10.1101\/gr.078212.108","volume":"18","author":"H Li","year":"2008","unstructured":"Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 2008, 18: 1851\u20131858. 10.1101\/gr.078212.108","journal-title":"Genome Research"},{"key":"3587_CR5","doi-asserted-by":"publisher","first-page":"e1000386","DOI":"10.1371\/journal.pcbi.1000386","volume":"5","author":"SM Rumble","year":"2009","unstructured":"Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M: SHRiMP: accurate mapping of short color-space reads. PLoS computational biology 2009, 5: e1000386. 10.1371\/journal.pcbi.1000386","journal-title":"PLoS computational biology"},{"key":"3587_CR6","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10: R25. 10.1186\/gb-2009-10-3-r25","journal-title":"Genome Biology"},{"key":"3587_CR7","volume-title":"Internet Request for Comments","author":"RL Rivest","year":"1992","unstructured":"Rivest RL: The MD5 Message-Digest Algorithm. Internet Request for Comments 1992. [RFC 1321] [RFC 1321]"},{"key":"3587_CR8","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1093\/bioinformatics\/bti774","volume":"22","author":"A Morgulis","year":"2006","unstructured":"Morgulis A, Gertz EM, Sch\u00e4ffer AA, Agarwala R: WindowMasker: window-based masker for sequenced genomes. Bioinformatics 2006, 22: 134\u2013141. 10.1093\/bioinformatics\/bti774","journal-title":"Bioinformatics"},{"key":"3587_CR9","volume-title":"PhD thesis","author":"RS Harris","year":"2007","unstructured":"Harris RS: Improved pairwise alignment of genomic DNA. PhD thesis. Penn State University, Computer Science and Engineering; 2007."},{"key":"3587_CR10","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1101\/gr.809403","volume":"13","author":"S Schwartz","year":"2003","unstructured":"Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W: Human-mouse alignments with BLASTZ. Genome Research 2003, 13: 103\u2013107. 10.1101\/gr.809403","journal-title":"Genome Research"},{"key":"3587_CR11","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature03959","volume":"437","author":"M Margulies","year":"2005","unstructured":"Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437: 376\u2013380.","journal-title":"Nature"},{"key":"3587_CR12","unstructured":"Consed 12.0 documentation[\n                    http:\/\/bcr.musc.edu\/manuals\/CONSED.txt\n                    \n                  ]"},{"key":"3587_CR13","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1038\/nature06884","volume":"452","author":"DA Wheeler","year":"2008","unstructured":"Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen Y, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song X, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M: The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452: 872\u2013876. 10.1038\/nature06884","journal-title":"Nature"},{"issue":"9","key":"3587_CR14","doi-asserted-by":"publisher","first-page":"1622","DOI":"10.1101\/gr.092197.109","volume":"19","author":"SM Ahn","year":"2009","unstructured":"Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ: The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group. Genome Research 2009, 19(9):1622\u20131629. 10.1101\/gr.092197.109","journal-title":"Genome Research"},{"key":"3587_CR15","doi-asserted-by":"publisher","first-page":"e72","DOI":"10.1371\/journal.pone.0000072","volume":"1","author":"S Bensch","year":"2006","unstructured":"Bensch S, Andr\u00e9n H, Hansson B, Pedersen H, Sand H, Sejberg D, Wabakken P, \u00c5kesson M, Liberg O: Selection for heterozygosity gives hope to a wild population of inbred wolves. PLoS ONE 2006, 1: e72. 10.1371\/journal.pone.0000072","journal-title":"PLoS ONE"},{"key":"3587_CR16","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1098\/rsbl.2008.0734","volume":"5","author":"JL Fitzpatrick","year":"2009","unstructured":"Fitzpatrick JL, Evans JP: Reduced heterozygosity impairs sperm quality in endangered mammals. Biology Letters 2009, 5: 320\u2013323. 10.1098\/rsbl.2008.0734","journal-title":"Biology Letters"},{"key":"3587_CR17","first-page":"43","volume":"15","author":"W Miller","year":"2010","unstructured":"Miller W, Wright SJ, Zhang Y, Schuster SC, Hayes V: Optimization methods for selecting founder populations for captive breeding of endangered species. Pacific Symposium on Biocomputing 2010, 15: 43\u201353.","journal-title":"Pacific Symposium on Biocomputing"},{"issue":"6803","key":"3587_CR18","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/35035083","volume":"407","author":"D Altshuler","year":"2000","unstructured":"Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES: An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 2000, 407(6803):513\u2013516. 10.1038\/35035083","journal-title":"Nature"},{"key":"3587_CR19","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1038\/nmeth.1185","volume":"5","author":"CPP Van Tassell","year":"2008","unstructured":"Van Tassell CPP, Smith TPLP, Matukumalli LKK, Taylor JFF, Schnabel RDD, Lawley CTT, Haudenschild CDD, Moore SSS, Warren WCC, Sonstegard TSS: SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods 2008, 5: 247\u2013252. 10.1038\/nmeth.1185","journal-title":"Nat Methods"},{"key":"3587_CR20","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/1471-2156-9-81","volume":"9","author":"R Wiedmann","year":"2008","unstructured":"Wiedmann R, Smith T, Nonneman D: SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genetics 2008, 9: 81. 10.1186\/1471-2156-9-81","journal-title":"BMC Genetics"},{"key":"3587_CR21","doi-asserted-by":"publisher","first-page":"374+","DOI":"10.1186\/1471-2164-10-374","volume":"10","author":"A Amaral","year":"2009","unstructured":"Amaral A, Megens HJ, Kerstens H, Heuven H, Dibbits B, Crooijmans R, den Dunnen J, Groenen M: Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics 2009, 10: 374+. 10.1186\/1471-2164-10-374","journal-title":"BMC Genomics"},{"key":"3587_CR22","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1186\/1471-2164-10-479","volume":"10","author":"H Kerstens","year":"2009","unstructured":"Kerstens H, Crooijmans R, Veenendaal A, Dibbits B, Chin-A-Woeng T, den Dunnen J, Groenen M: Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genomics 2009, 10: 479. 10.1186\/1471-2164-10-479","journal-title":"BMC Genomics"},{"key":"3587_CR23","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1038\/nmeth1111","volume":"4","author":"TJ Albert","year":"2007","unstructured":"Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA: Direct selection of human genomic loci by microarray hybridization. Nat Meth 2007, 4: 903\u2013905. 10.1038\/nmeth1111","journal-title":"Nat Meth"},{"issue":"2","key":"3587_CR24","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/nbt.1523","volume":"27","author":"A Gnirke","year":"2009","unstructured":"Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature biotechnology 2009, 27(2):182\u2013189. 10.1038\/nbt.1523","journal-title":"Nature biotechnology"},{"key":"3587_CR25","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1126\/science.307.5712.1035","volume":"307","author":"A Bostanci","year":"2005","unstructured":"Bostanci A: Wildlife biology: A devil of a disease. Science 2005, 307: 1035. 10.1126\/science.307.5712.1035","journal-title":"Science"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-11-130\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-130.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T12:55:39Z","timestamp":1548161739000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-130"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,15]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3587"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-130","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,3,15]]},"article-number":"130"}}