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Items: 1 to 20 of 105

1.

From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.

Camerlengo T, Ozer HG, Onti-Srinivasan R, Yan P, Huang T, Parvin J, Huang K.

AMIA Jt Summits Transl Sci Proc. 2012;2012:1-10. Epub 2012 Mar 19.

2.

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O.

Gigascience. 2015 Jun 4;4:26. doi: 10.1186/s13742-015-0058-5. eCollection 2015. Erratum in: Gigascience. 2015;4:61.

3.

Next generation distributed computing for cancer research.

Agarwal P, Owzar K.

Cancer Inform. 2015 Apr 27;13(Suppl 7):97-109. doi: 10.4137/CIN.S16344. eCollection 2014. Review.

4.

DDBJ read annotation pipeline: a cloud computing-based pipeline for high-throughput analysis of next-generation sequencing data.

Nagasaki H, Mochizuki T, Kodama Y, Saruhashi S, Morizaki S, Sugawara H, Ohyanagi H, Kurata N, Okubo K, Takagi T, Kaminuma E, Nakamura Y.

DNA Res. 2013 Aug;20(4):383-90. doi: 10.1093/dnares/dst017. Epub 2013 May 8.

5.

BING: biomedical informatics pipeline for Next Generation Sequencing.

Kriseman J, Busick C, Szelinger S, Dinu V.

J Biomed Inform. 2010 Jun;43(3):428-34. doi: 10.1016/j.jbi.2009.11.003. Epub 2009 Nov 28.

6.

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data.

Katta MA, Khan AW, Doddamani D, Thudi M, Varshney RK.

PLoS One. 2015 Oct 13;10(10):e0139868. doi: 10.1371/journal.pone.0139868. eCollection 2015.

7.

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis.

Velmeshev D, Lally P, Magistri M, Faghihi MA.

BMC Genomics. 2016 Jan 13;17:49. doi: 10.1186/s12864-015-2346-y.

8.

OTP: An automatized system for managing and processing NGS data.

Reisinger E, Genthner L, Kerssemakers J, Kensche P, Borufka S, Jugold A, Kling A, Prinz M, Scholz I, Zipprich G, Eils R, Lawerenz C, Eils J.

J Biotechnol. 2017 Nov 10;261:53-62. doi: 10.1016/j.jbiotec.2017.08.006. Epub 2017 Aug 10.

9.

Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

Kim B, Ali T, Lijeron C, Afgan E, Krampis K.

Gigascience. 2017 Aug 1;6(8):1-7. doi: 10.1093/gigascience/gix048.

10.

Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

Bailey SF, Scheible MK, Williams C, Silva DSBS, Hoggan M, Eichman C, Faith SA.

Forensic Sci Int Genet. 2017 Nov;31:40-47. doi: 10.1016/j.fsigen.2017.08.008. Epub 2017 Aug 8.

PMID:
28837856
11.

Cluster Flow: A user-friendly bioinformatics workflow tool.

Ewels P, Krueger F, Käller M, Andrews S.

Version 2. F1000Res. 2016 Dec 6 [revised 2017 Jan 1];5:2824. doi: 10.12688/f1000research.10335.2. eCollection 2016.

12.

A distributed system for fast alignment of next-generation sequencing data.

Srimani JK, Wu PY, Phan JH, Wang MD.

IEEE Int Conf Bioinform Biomed Workshops. 2010 Dec;2010:579-584.

13.

A simple grid implementation with Berkeley Open Infrastructure for Network Computing using BLAST as a model.

Pinthong W, Muangruen P, Suriyaphol P, Mairiang D.

PeerJ. 2016 Jul 28;4:e2248. doi: 10.7717/peerj.2248. eCollection 2016.

14.

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform.

Kilianski A, Carcel P, Yao S, Roth P, Schulte J, Donarum GB, Fochler ET, Hill JM, Liem AT, Wiley MR, Ladner JT, Pfeffer BP, Elliot O, Petrosov A, Jima DD, Vallard TG, Melendrez MC, Skowronski E, Quan PL, Lipkin WI, Gibbons HS, Hirschberg DL, Palacios GF, Rosenzweig CN.

BMC Bioinformatics. 2015 Dec 29;16:416. doi: 10.1186/s12859-015-0840-5.

15.

Applications of the pipeline environment for visual informatics and genomics computations.

Dinov ID, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW.

BMC Bioinformatics. 2011 Jul 26;12:304. doi: 10.1186/1471-2105-12-304.

16.

preAssemble: a tool for automatic sequencer trace data processing.

Adzhubei AA, Laerdahl JK, Vlasova AV.

BMC Bioinformatics. 2006 Jan 17;7:22.

17.

Lane-by-lane sequencing using Illumina's Genome Analyzer II.

Gravina MT, Lin JH, Levine SS.

Biotechniques. 2013 May;54(5):265-9. doi: 10.2144/000114032.

18.

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

Wu TJ, Shamsaddini A, Pan Y, Smith K, Crichton DJ, Simonyan V, Mazumder R.

Database (Oxford). 2014 Mar 25;2014:bau022. doi: 10.1093/database/bau022. Print 2014.

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.

20.

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