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Items: 1 to 20 of 176

1.

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.

2.

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.

3.

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.

4.

Amplicon Indel Hunter Is a Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based Next-Generation Sequencing Data.

Kadri S, Zhen CJ, Wurst MN, Long BC, Jiang ZF, Wang YL, Furtado LV, Segal JP.

J Mol Diagn. 2015 Nov;17(6):635-43. doi: 10.1016/j.jmoldx.2015.06.005. Epub 2015 Aug 28.

PMID:
26319364
5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

Comparison of insertion/deletion calling algorithms on human next-generation sequencing data.

Ghoneim DH, Myers JR, Tuttle E, Paciorkowski AR.

BMC Res Notes. 2014 Dec 1;7:864. doi: 10.1186/1756-0500-7-864.

12.

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 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.

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.

15.

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.

16.

SIFT Indel: predictions for the functional effects of amino acid insertions/deletions in proteins.

Hu J, Ng PC.

PLoS One. 2013 Oct 23;8(10):e77940. doi: 10.1371/journal.pone.0077940. eCollection 2013.

17.

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
18.

Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.

Tae H, Settlage RE, Shallom S, Bavarva JH, Preston D, Hawkins GN, Adams LG, Garner HR.

Genomics. 2012 Nov;100(5):271-6. doi: 10.1016/j.ygeno.2012.07.015. Epub 2012 Aug 10.

19.
20.

Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations.

Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JA.

Brief Bioinform. 2016 Jul 29. pii: bbw069. [Epub ahead of print]

PMID:
27473065

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