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Items: 1 to 20 of 135


SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.

Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP.

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.


Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

Samadian S, Bruce JP, Pugh TJ.

PLoS Comput Biol. 2018 Mar 28;14(3):e1006080. doi: 10.1371/journal.pcbi.1006080. eCollection 2018 Mar.


UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing.

Park DJ, Li R, Lau E, Georgeson P, Nguyen-Dumont T, Pope BJ.

BMC Bioinformatics. 2016 Apr 16;17:165. doi: 10.1186/s12859-016-1014-9.


Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models.

Stephens ZD, Hudson ME, Mainzer LS, Taschuk M, Weber MR, Iyer RK.

PLoS One. 2016 Nov 28;11(11):e0167047. doi: 10.1371/journal.pone.0167047. eCollection 2016.


Calling known variants and identifying new variants while rapidly aligning sequence data.

VanRaden PM, Bickhart DM, O'Connell JR.

J Dairy Sci. 2019 Apr;102(4):3216-3229. doi: 10.3168/jds.2018-15172. Epub 2019 Feb 14.


SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B.

BMC Bioinformatics. 2014 Feb 5;15:40. doi: 10.1186/1471-2105-15-40.


VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.

Mu JC, Mohiyuddin M, Li J, Bani Asadi N, Gerstein MB, Abyzov A, Wong WH, Lam HY.

Bioinformatics. 2015 May 1;31(9):1469-71. doi: 10.1093/bioinformatics/btu828. Epub 2014 Dec 17.


BIMA V3: an aligner customized for mate pair library sequencing.

Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G.

Bioinformatics. 2014 Jun 1;30(11):1627-9. doi: 10.1093/bioinformatics/btu078. Epub 2014 Feb 12.


InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.

Patel A, Edge P, Selvaraj S, Bansal V, Bafna V.

Nucleic Acids Res. 2016 Jul 8;44(12):e111. doi: 10.1093/nar/gkw281. Epub 2016 Apr 21.


INDELseek: detection of complex insertions and deletions from next-generation sequencing data.

Au CH, Leung AY, Kwong A, Chan TL, Ma ES.

BMC Genomics. 2017 Jan 5;18(1):16. doi: 10.1186/s12864-016-3449-9.


NanoSim: nanopore sequence read simulator based on statistical characterization.

Yang C, Chu J, Warren RL, Birol I.

Gigascience. 2017 Apr 1;6(4):1-6. doi: 10.1093/gigascience/gix010.


Toolkit for automated and rapid discovery of structural variants.

Soylev A, Kockan C, Hormozdiari F, Alkan C.

Methods. 2017 Oct 1;129:3-7. doi: 10.1016/j.ymeth.2017.05.030. Epub 2017 Jun 2.


Towards accurate characterization of clonal heterogeneity based on structural variation.

Fan X, Zhou W, Chong Z, Nakhleh L, Chen K.

BMC Bioinformatics. 2014 Sep 8;15:299. doi: 10.1186/1471-2105-15-299.


Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, Cox AJ, Kruglyak S, Saunders CT.

Bioinformatics. 2016 Apr 15;32(8):1220-2. doi: 10.1093/bioinformatics/btv710. Epub 2015 Dec 8.


Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.

Gillet-Markowska A, Richard H, Fischer G, Lafontaine I.

Bioinformatics. 2015 Mar 15;31(6):801-8. doi: 10.1093/bioinformatics/btu730. Epub 2014 Nov 7.


Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG.

BMC Genomics. 2014 Nov 29;15:1039. doi: 10.1186/1471-2164-15-1039.


svclassify: a method to establish benchmark structural variant calls.

Parikh H, Mohiyuddin M, Lam HY, Iyer H, Chen D, Pratt M, Bartha G, Spies N, Losert W, Zook JM, Salit M.

BMC Genomics. 2016 Jan 16;17:64. doi: 10.1186/s12864-016-2366-2.


ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

Coombe L, Zhang J, Vandervalk BP, Chu J, Jackman SD, Birol I, Warren RL.

BMC Bioinformatics. 2018 Jun 20;19(1):234. doi: 10.1186/s12859-018-2243-x.


RAPTR-SV: a hybrid method for the detection of structural variants.

Bickhart DM, Hutchison JL, Xu L, Schnabel RD, Taylor JF, Reecy JM, Schroeder S, Van Tassell CP, Sonstegard TS, Liu GE.

Bioinformatics. 2015 Jul 1;31(13):2084-90. doi: 10.1093/bioinformatics/btv086. Epub 2015 Feb 16.


Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.

Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC.

Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5.

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