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Items: 1 to 20 of 115

1.

Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data.

Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW.

PLoS Comput Biol. 2013 Apr;9(4):e1003031. doi: 10.1371/journal.pcbi.1003031. Epub 2013 Apr 11.

2.

Pollux: platform independent error correction of single and mixed genomes.

Marinier E, Brown DG, McConkey BJ.

BMC Bioinformatics. 2015 Jan 16;16:10. doi: 10.1186/s12859-014-0435-6.

3.

Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes.

Yeo ZX, Wong JC, Rozen SG, Lee AS.

BMC Genomics. 2014 Jun 24;15:516. doi: 10.1186/1471-2164-15-516.

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.

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.

Caboche S, Audebert C, Lemoine Y, Hot D.

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.

6.

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH.

Zhang B, Penton CR, Xue C, Wang Q, Zheng T, Tiedje JM.

Appl Environ Microbiol. 2015 Jul;81(13):4536-45. doi: 10.1128/AEM.00111-15. Epub 2015 Apr 24.

7.

Blue: correcting sequencing errors using consensus and context.

Greenfield P, Duesing K, Papanicolaou A, Bauer DC.

Bioinformatics. 2014 Oct;30(19):2723-32. doi: 10.1093/bioinformatics/btu368. Epub 2014 Jun 11.

PMID:
24919879
8.

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.

9.

Detection of variations and identifying genomic breakpoints for large deletions in the LDLR by Ion Torrent semiconductor sequencing.

Faiz F, Allcock RJ, Hooper AJ, van Bockxmeer FM.

Atherosclerosis. 2013 Oct;230(2):249-55. doi: 10.1016/j.atherosclerosis.2013.07.050. Epub 2013 Aug 4.

PMID:
24075752
10.

Performance comparison of benchtop high-throughput sequencing platforms.

Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ.

Nat Biotechnol. 2012 May;30(5):434-9. doi: 10.1038/nbt.2198. Erratum in: Nat Biotechnol. 2012 Jun;30(6):562.

PMID:
22522955
11.

Performance characteristics of the AmpliSeq Cancer Hotspot panel v2 in combination with the Ion Torrent Next Generation Sequencing Personal Genome Machine.

Butler KS, Young MY, Li Z, Elespuru RK, Wood SC.

Regul Toxicol Pharmacol. 2016 Feb;74:178-86. doi: 10.1016/j.yrtph.2015.09.011. Epub 2015 Sep 24.

PMID:
26387931
12.

[Detection of pathogenic mutations in Marfan syndrome by targeted next-generation semiconductor sequencing].

Lu C, Wu W, Xiao J, Meng Y, Zhang S, Zhang X.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2013 Jun;30(3):301-4. doi: 10.3760/cma.j.issn.1003-9406.2013.03.011. Chinese.

PMID:
23744319
13.

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.

14.

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data.

Allam A, Kalnis P, Solovyev V.

Bioinformatics. 2015 Nov 1;31(21):3421-8. doi: 10.1093/bioinformatics/btv415. Epub 2015 Jul 14.

PMID:
26177965
15.

[Screening for genetic mutations in hyperphenylalaninemia using Ion Torrent PGM sequencing].

Cao Y, Qu Y, Song F, Bai J, Jin Y, Wang H.

Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2015 Feb;32(1):16-20. doi: 10.3760/cma.j.issn.1003-9406.2015.01.004. Chinese.

PMID:
25636092
16.

Quality score based identification and correction of pyrosequencing errors.

Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI.

PLoS One. 2013 Sep 5;8(9):e73015. doi: 10.1371/journal.pone.0073015. eCollection 2013.

17.

Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2.

Hwang SM, Lee KC, Lee MS, Park KU.

Cancer Res Treat. 2017 Apr 7. doi: 10.4143/crt.2017.062. [Epub ahead of print]

18.

Reducing INDEL calling errors in whole genome and exome sequencing data.

Fang H, Wu Y, Narzisi G, O'Rawe JA, Barrón LT, Rosenbaum J, Ronemus M, Iossifov I, Schatz MC, Lyon GJ.

Genome Med. 2014 Oct 28;6(10):89. doi: 10.1186/s13073-014-0089-z. eCollection 2014.

19.

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.

Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, Salit M.

Nat Biotechnol. 2014 Mar;32(3):246-51. doi: 10.1038/nbt.2835. Epub 2014 Feb 16.

PMID:
24531798
20.

Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

Vogel U, Szczepanowski R, Claus H, Jünemann S, Prior K, Harmsen D.

J Clin Microbiol. 2012 Jun;50(6):1889-94. doi: 10.1128/JCM.00038-12. Epub 2012 Mar 29.

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