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Items: 1 to 20 of 205

1.

PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants.

Jiang Y, Wang Y, Brudno M.

Bioinformatics. 2012 Oct 15;28(20):2576-83. doi: 10.1093/bioinformatics/bts484. Epub 2012 Jul 31.

PMID:
22851530
2.

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

Emde AK, Schulz MH, Weese D, Sun R, Vingron M, Kalscheuer VM, Haas SA, Reinert K.

Bioinformatics. 2012 Mar 1;28(5):619-27. doi: 10.1093/bioinformatics/bts019. Epub 2012 Jan 11.

PMID:
22238266
3.

DELLY: structural variant discovery by integrated paired-end and split-read analysis.

Rausch T, Zichner T, Schlattl A, Stütz AM, Benes V, Korbel JO.

Bioinformatics. 2012 Sep 15;28(18):i333-i339. doi: 10.1093/bioinformatics/bts378.

4.

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

Zhang J, Wang J, Wu Y.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6. doi: 10.1186/1471-2105-13-S6-S6.

5.

Robust and exact structural variation detection with paired-end and soft-clipped alignments: SoftSV compared with eight algorithms.

Bartenhagen C, Dugas M.

Brief Bioinform. 2016 Jan;17(1):51-62. doi: 10.1093/bib/bbv028. Epub 2015 May 20.

PMID:
25998133
6.

SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data.

Zhang J, Wu Y.

Bioinformatics. 2011 Dec 1;27(23):3228-34. doi: 10.1093/bioinformatics/btr563. Epub 2011 Oct 12.

PMID:
21994222
7.

Identification of genomic indels and structural variations using split reads.

Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M.

BMC Genomics. 2011 Jul 25;12:375. doi: 10.1186/1471-2164-12-375.

8.

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.

PMID:
25686638
9.

SVM²: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data.

Chiara M, Pesole G, Horner DS.

Nucleic Acids Res. 2012 Oct;40(18):e145. doi: 10.1093/nar/gks606. Epub 2012 Jun 25.

10.

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.

Trappe K, Emde AK, Ehrlich HC, Reinert K.

Bioinformatics. 2014 Dec 15;30(24):3484-90. doi: 10.1093/bioinformatics/btu431. Epub 2014 Jul 14.

PMID:
25028727
11.

Detecting copy number variation with mated short reads.

Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.

Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30.

12.

BatAlign: an incremental method for accurate alignment of sequencing reads.

Lim JQ, Tennakoon C, Guan P, Sung WK.

Nucleic Acids Res. 2015 Sep 18;43(16):e107. doi: 10.1093/nar/gkv533. Epub 2015 Jul 13.

13.

Bellerophon: a hybrid method for detecting interchromosomal rearrangements at base pair resolution using next-generation sequencing data.

Hayes M, Li J.

BMC Bioinformatics. 2013;14 Suppl 5:S6. doi: 10.1186/1471-2105-14-S5-S6. Epub 2013 Apr 10.

14.

Detection of structural variants involving repetitive regions in the reference genome.

Lee H, Popodi E, Foster PL, Tang H.

J Comput Biol. 2014 Mar;21(3):219-33. doi: 10.1089/cmb.2013.0129. Epub 2014 Feb 19.

PMID:
24552580
15.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
16.

Next generation mapping reveals novel large genomic rearrangements in prostate cancer.

Jaratlerdsiri W, Chan EKF, Petersen DC, Yang C, Croucher PI, Bornman MSR, Sheth P, Hayes VM.

Oncotarget. 2017 Apr 4;8(14):23588-23602. doi: 10.18632/oncotarget.15802.

17.

Characterization of structural variants with single molecule and hybrid sequencing approaches.

Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.

Bioinformatics. 2014 Dec 15;30(24):3458-66. doi: 10.1093/bioinformatics/btu714. Epub 2014 Oct 28.

18.

Identification of indels in next-generation sequencing data.

Ratan A, Olson TL, Loughran TP Jr, Miller W.

BMC Bioinformatics. 2015 Feb 13;16:42. doi: 10.1186/s12859-015-0483-6.

19.

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees.

Mahmud MP, Wiedenhoeft J, Schliep A.

Bioinformatics. 2012 Sep 15;28(18):i325-i332. doi: 10.1093/bioinformatics/bts380.

20.

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data.

Qi J, Zhao F.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W567-75. doi: 10.1093/nar/gkr506.

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