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Items: 1 to 20 of 162


Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias.

McElroy K, Zagordi O, Bull R, Luciani F, Beerenwinkel N.

BMC Genomics. 2013 Jul 24;14:501. doi: 10.1186/1471-2164-14-501.


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.


Dindel: accurate indel calls from short-read data.

Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R.

Genome Res. 2011 Jun;21(6):961-73. doi: 10.1101/gr.112326.110. Epub 2010 Oct 27.


ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering.

Verbist B, Clement L, Reumers J, Thys K, Vapirev A, Talloen W, Wetzels Y, Meys J, Aerssens J, Bijnens L, Thas O.

BMC Bioinformatics. 2015 Feb 22;16:59. doi: 10.1186/s12859-015-0458-7.


Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals.

Cheng AY, Teo YY, Ong RT.

Bioinformatics. 2014 Jun 15;30(12):1707-13. doi: 10.1093/bioinformatics/btu067. Epub 2014 Feb 19.


Whole genome sequencing of 35 individuals provides insights into the genetic architecture of Korean population.

Zhang W, Meehan J, Su Z, Ng HW, Shu M, Luo H, Ge W, Perkins R, Tong W, Hong H.

BMC Bioinformatics. 2014;15 Suppl 11:S6. doi: 10.1186/1471-2105-15-S11-S6. Epub 2014 Oct 21.


Aligning to the sample-specific reference sequence to optimize the accuracy of next-generation sequencing analysis for hepatitis B virus.

Liu WC, Lin CP, Cheng CP, Ho CH, Lan KL, Cheng JH, Yen CJ, Cheng PN, Wu IC, Li IC, Chang BC, Tseng VS, Chiu YC, Chang TT.

Hepatol Int. 2016 Jan;10(1):147-57. doi: 10.1007/s12072-015-9645-x. Epub 2015 Jul 25.


SNVHMM: predicting single nucleotide variants from next generation sequencing.

Bian J, Liu C, Wang H, Xing J, Kachroo P, Zhou X.

BMC Bioinformatics. 2013 Jul 15;14:225. doi: 10.1186/1471-2105-14-225.


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.


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.


Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.

Duitama J, Srivastava PK, Măndoiu II.

BMC Genomics. 2012 Apr 12;13 Suppl 2:S6. doi: 10.1186/1471-2164-13-S2-S6.


Revising a personal genome by comparing and combining data from two different sequencing platforms.

Kim D, Kim WY, Lee SY, Lee SY, Yun H, Shin SY, Lee J, Hong Y, Won Y, Kim SJ, Lee YS, Ahn SM.

PLoS One. 2013 Apr 8;8(4):e60585. doi: 10.1371/journal.pone.0060585. Print 2013.


Comparison of sequencing platforms for single nucleotide variant calls in a human sample.

Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC.

PLoS One. 2013;8(2):e55089. doi: 10.1371/journal.pone.0055089. Epub 2013 Feb 6.


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.


An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

Wang Y, Lu J, Yu J, Gibbs RA, Yu F.

Genome Res. 2013 May;23(5):833-42. doi: 10.1101/gr.146084.112. Epub 2013 Jan 7.


ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.

Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N.

BMC Bioinformatics. 2011 Apr 26;12:119. doi: 10.1186/1471-2105-12-119.


Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.


SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.


Viral quasispecies assembly via maximal clique enumeration.

Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515. eCollection 2014 Mar.


VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.

Verbist BM, Thys K, Reumers J, Wetzels Y, Van der Borght K, Talloen W, Aerssens J, Clement L, Thas O.

Bioinformatics. 2015 Jan 1;31(1):94-101. doi: 10.1093/bioinformatics/btu587. Epub 2014 Aug 31.


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