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Items: 1 to 20 of 167


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.


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.


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.


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.


Vindel: a simple pipeline for checking indel redundancy.

Li Z, Wu X, He B, Zhang L.

BMC Bioinformatics. 2014 Nov 19;15:359. doi: 10.1186/s12859-014-0359-1.


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.


WEP: a high-performance analysis pipeline for whole-exome data.

D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.

BMC Bioinformatics. 2013;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.


Performance evaluation of indel calling tools using real short-read data.

Hasan MS, Wu X, Zhang L.

Hum Genomics. 2015 Aug 19;9:20. doi: 10.1186/s40246-015-0042-2.


Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.

Ye K, Schulz MH, Long Q, Apweiler R, Ning Z.

Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.


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.


A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population.

Pelleymounter LL, Moon I, Johnson JA, Laederach A, Halvorsen M, Eckloff B, Abo R, Rossetti S.

Mol Genet Metab. 2011 Dec;104(4):457-69. doi: 10.1016/j.ymgme.2011.08.019. Epub 2011 Aug 24.


Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer.

Yeo ZX, Chan M, Yap YS, Ang P, Rozen S, Lee AS.

PLoS One. 2012;7(9):e45798. doi: 10.1371/journal.pone.0045798. Epub 2012 Sep 19.


The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes.

Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G, Yu F.

BMC Genomics. 2015 Feb 28;16:143. doi: 10.1186/s12864-015-1333-7.


SOAPindel: efficient identification of indels from short paired reads.

Li S, Li R, Li H, Lu J, Li Y, Bolund L, Schierup MH, Wang J.

Genome Res. 2013 Jan;23(1):195-200. doi: 10.1101/gr.132480.111. Epub 2012 Sep 12.


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.


ABRA: improved coding indel detection via assembly-based realignment.

Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.

Bioinformatics. 2014 Oct;30(19):2813-5. doi: 10.1093/bioinformatics/btu376. Epub 2014 Jun 6.


ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.

Blanca JM, Pascual L, Ziarsolo P, Nuez F, Cañizares J.

BMC Genomics. 2011 Jun 2;12:285. doi: 10.1186/1471-2164-12-285.


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.


MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT.

PLoS One. 2014 Mar 5;9(3):e90581. doi: 10.1371/journal.pone.0090581. eCollection 2014.


Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.

Hamada M, Wijaya E, Frith MC, Asai K.

Bioinformatics. 2011 Nov 15;27(22):3085-92. doi: 10.1093/bioinformatics/btr537. Epub 2011 Oct 5.

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