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Items: 1 to 20 of 86

1.

CLEVER: clique-enumerating variant finder.

Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A.

Bioinformatics. 2012 Nov 15;28(22):2875-82. doi: 10.1093/bioinformatics/bts566. Epub 2012 Oct 11.

PMID:
23060616
2.

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels.

Marschall T, Hajirasouliha I, Schönhuth A.

Bioinformatics. 2013 Dec 15;29(24):3143-50. doi: 10.1093/bioinformatics/btt556. Epub 2013 Sep 25.

3.

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
4.

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.

5.

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
6.

Long read alignment based on maximal exact match seeds.

Liu Y, Schmidt B.

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

7.

Accurate indel prediction using paired-end short reads.

Grimm D, Hagmann J, Koenig D, Weigel D, Borgwardt K.

BMC Genomics. 2013 Feb 27;14:132. doi: 10.1186/1471-2164-14-132.

8.

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
9.

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.

Bansal V, Libiger O.

Bioinformatics. 2011 Aug 1;27(15):2047-53. doi: 10.1093/bioinformatics/btr344. Epub 2011 Jun 7.

10.

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
11.

Microindel detection in short-read sequence data.

Krawitz P, Rödelsperger C, Jäger M, Jostins L, Bauer S, Robinson PN.

Bioinformatics. 2010 Mar 15;26(6):722-9. doi: 10.1093/bioinformatics/btq027. Epub 2010 Feb 9.

PMID:
20144947
12.

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.

13.

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.

14.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

15.

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes.

Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Genome Res. 2009 Jul;19(7):1270-8. doi: 10.1101/gr.088633.108. Epub 2009 May 15.

16.

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
18.

GASSST: global alignment short sequence search tool.

Rizk G, Lavenier D.

Bioinformatics. 2010 Oct 15;26(20):2534-40. doi: 10.1093/bioinformatics/btq485. Epub 2010 Aug 24.

19.

A robust framework for detecting structural variations in a genome.

Lee S, Cheran E, Brudno M.

Bioinformatics. 2008 Jul 1;24(13):i59-67. doi: 10.1093/bioinformatics/btn176.

20.

Structural variation analysis with strobe reads.

Ritz A, Bashir A, Raphael BJ.

Bioinformatics. 2010 May 15;26(10):1291-8. doi: 10.1093/bioinformatics/btq153. Epub 2010 Apr 8.

PMID:
20378554

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