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1.

QPLOT: a quality assessment tool for next generation sequencing data.

Li B, Zhan X, Wing MK, Anderson P, Kang HM, Abecasis GR.

Biomed Res Int. 2013;2013:865181. doi: 10.1155/2013/865181. Epub 2013 Nov 11.

2.

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data.

Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN.

BMC Bioinformatics. 2012 Sep 4;13:221.

3.

Qualimap: evaluating next-generation sequencing alignment data.

García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A.

Bioinformatics. 2012 Oct 15;28(20):2678-9. doi: 10.1093/bioinformatics/bts503. Epub 2012 Aug 22.

4.

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data.

Peng Y, Maxwell AS, Barker ND, Laird JG, Kennedy AJ, Wang N, Zhang C, Gong P.

BMC Bioinformatics. 2014;15 Suppl 11:S10. doi: 10.1186/1471-2105-15-S11-S10. Epub 2014 Oct 21.

5.

Multi-perspective quality control of Illumina exome sequencing data using QC3.

Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y.

Genomics. 2014 May-Jun;103(5-6):323-8. doi: 10.1016/j.ygeno.2014.03.006. Epub 2014 Apr 3.

PMID:
24703969
6.

BamView: visualizing and interpretation of next-generation sequencing read alignments.

Carver T, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA.

Brief Bioinform. 2013 Mar;14(2):203-12. doi: 10.1093/bib/bbr073. Epub 2012 Jan 16.

7.

Quantifying uniformity of mapped reads.

Hower V, Starfield R, Roberts A, Pachter L.

Bioinformatics. 2012 Oct 15;28(20):2680-2. doi: 10.1093/bioinformatics/bts451. Epub 2012 Jul 18.

8.
9.

QC-Chain: fast and holistic quality control method for next-generation sequencing data.

Zhou Q, Su X, Wang A, Xu J, Ning K.

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.

10.

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, Reich M, Winckler W, Getz G.

Bioinformatics. 2012 Jun 1;28(11):1530-2. doi: 10.1093/bioinformatics/bts196. Epub 2012 Apr 25.

11.

SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

Sato Y, Kojima K, Nariai N, Yamaguchi-Kabata Y, Kawai Y, Takahashi M, Mimori T, Nagasaki M.

BMC Genomics. 2014 Aug 8;15:664. doi: 10.1186/1471-2164-15-664.

12.

BIGpre: a quality assessment package for next-generation sequencing data.

Zhang T, Luo Y, Liu K, Pan L, Zhang B, Yu J, Hu S.

Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44. doi: 10.1016/S1672-0229(11)60027-2.

13.

Customisation of the exome data analysis pipeline using a combinatorial approach.

Pattnaik S, Vaidyanathan S, Pooja DG, Deepak S, Panda B.

PLoS One. 2012;7(1):e30080. doi: 10.1371/journal.pone.0030080. Epub 2012 Jan 6.

14.

Impact of the next-generation sequencing data depth on various biological result inferences.

Hou R, Yang Z, Li M, Xiao H.

Sci China Life Sci. 2013 Feb;56(2):104-9. doi: 10.1007/s11427-013-4441-0. Epub 2013 Feb 8. Review.

PMID:
23393025
15.

SMITH: a LIMS for handling next-generation sequencing workflows.

Venco F, Vaskin Y, Ceol A, Muller H.

BMC Bioinformatics. 2014;15 Suppl 14:S3. doi: 10.1186/1471-2105-15-S14-S3. Epub 2014 Nov 27.

16.

Combinational usage of next generation sequencing and qPCR for the analysis of tumor samples.

Loewe RP.

Methods. 2013 Jan;59(1):126-31. doi: 10.1016/j.ymeth.2012.11.002. Epub 2012 Nov 21. Review.

PMID:
23178393
17.

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.

18.

NGSQC: cross-platform quality analysis pipeline for deep sequencing data.

Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S7. doi: 10.1186/1471-2164-11-S4-S7.

19.

A solid quality-control analysis of AB SOLiD short-read sequencing data.

Castellana S, Romani M, Valente EM, Mazza T.

Brief Bioinform. 2013 Nov;14(6):684-95. doi: 10.1093/bib/bbs048. Epub 2012 Aug 9.

PMID:
22877770
20.

Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM).

Parson W, Strobl C, Huber G, Zimmermann B, Gomes SM, Souto L, Fendt L, Delport R, Langit R, Wootton S, Lagacé R, Irwin J.

Forensic Sci Int Genet. 2013 Sep;7(5):543-9. doi: 10.1016/j.fsigen.2013.06.003. Epub 2013 Jul 23.

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