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Items: 1 to 20 of 138


A SNP discovery method to assess variant allele probability from next-generation resequencing data.

Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F.

Genome Res. 2010 Feb;20(2):273-80. doi: 10.1101/gr.096388.109. Epub 2009 Dec 17.


SNP calling by sequencing pooled samples.

Raineri E, Ferretti L, Esteve-Codina A, Nevado B, Heath S, Pérez-Enciso M.

BMC Bioinformatics. 2012 Sep 20;13:239. doi: 10.1186/1471-2105-13-239.


BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.

Cantarel BL, Weaver D, McNeill N, Zhang J, Mackey AJ, Reese J.

BMC Bioinformatics. 2014 Apr 12;15:104. doi: 10.1186/1471-2105-15-104.


A statistical method for the detection of variants from next-generation resequencing of DNA pools.

Bansal V.

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214. Erratum in: Bioinformatics. 2016 Oct 15;32(20):3213.


SNP detection for massively parallel whole-genome resequencing.

Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J.

Genome Res. 2009 Jun;19(6):1124-32. doi: 10.1101/gr.088013.108. Epub 2009 May 6.


BM-SNP: A Bayesian Model for SNP Calling Using High Throughput Sequencing Data.

Xu Y, Zheng X, Yuan Y, Estecio MR, Issa JP, Qiu P, Ji Y, Liang S.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Nov-Dec;11(6):1038-44. doi: 10.1109/TCBB.2014.2321407.


ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

Souaiaia T, Frazier Z, Chen T.

J Comput Biol. 2011 Jun;18(6):795-807. doi: 10.1089/cmb.2011.0027. Epub 2011 May 12.


SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples.

Le SQ, Durbin R.

Genome Res. 2011 Jun;21(6):952-60. doi: 10.1101/gr.113084.110. Epub 2010 Oct 27.


Enriching targeted sequencing experiments for rare disease alleles.

Edwards TL, Song Z, Li C.

Bioinformatics. 2011 Aug 1;27(15):2112-8. doi: 10.1093/bioinformatics/btr324. Epub 2011 Jun 23.


Single-variant and multi-variant trend tests for genetic association with next-generation sequencing that are robust to sequencing error.

Kim W, Londono D, Zhou L, Xing J, Nato AQ, Musolf A, Matise TC, Finch SJ, Gordon D.

Hum Hered. 2012;74(3-4):172-83. doi: 10.1159/000346824. Epub 2013 Apr 11.


QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles.

Van der Borght K, Thys K, Wetzels Y, Clement L, Verbist B, Reumers J, van Vlijmen H, Aerssens J.

BMC Bioinformatics. 2015 Nov 10;16:379. doi: 10.1186/s12859-015-0812-9.


A cross-sample statistical model for SNP detection in short-read sequencing data.

Muralidharan O, Natsoulis G, Bell J, Newburger D, Xu H, Kela I, Ji H, Zhang N.

Nucleic Acids Res. 2012 Jan;40(1):e5. doi: 10.1093/nar/gkr851. Epub 2011 Nov 7.


GemSIM: general, error-model based simulator of next-generation sequencing data.

McElroy KE, Luciani F, Thomas T.

BMC Genomics. 2012 Feb 15;13:74. doi: 10.1186/1471-2164-13-74.


Analysis of context-dependent errors for illumina sequencing.

Abnizova I, Leonard S, Skelly T, Brown A, Jackson D, Gourtovaia M, Qi G, Te Boekhorst R, Faruque N, Lewis K, Cox T.

J Bioinform Comput Biol. 2012 Apr;10(2):1241005. doi: 10.1142/S0219720012410053.


An empirical Bayes mixture model for SNP detection in pooled sequencing data.

Zhou B.

Bioinformatics. 2012 Oct 15;28(20):2569-75. doi: 10.1093/bioinformatics/bts501. Epub 2012 Aug 22.


Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout.

Boussaha M, Guyomard R, Cabau C, Esquerré D, Quillet E.

BMC Genomics. 2012 Jun 13;13:238. doi: 10.1186/1471-2164-13-238.


LOCAS--a low coverage assembly tool for resequencing projects.

Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH.

PLoS One. 2011;6(8):e23455. doi: 10.1371/journal.pone.0023455. Epub 2011 Aug 15.


SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.

Van Tassell CP, Smith TP, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS.

Nat Methods. 2008 Mar;5(3):247-52. doi: 10.1038/nmeth.1185. Epub 2008 Feb 24.


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