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Items: 1 to 20 of 419

1.

SeqWare Query Engine: storing and searching sequence data in the cloud.

O'Connor BD, Merriman B, Nelson SF.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S2. doi: 10.1186/1471-2105-11-S12-S2.

2.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

Chung WC, Chen CC, Ho JM, Lin CY, Hsu WL, Wang YC, Lee DT, Lai F, Huang CW, Chang YJ.

PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146. eCollection 2014.

3.

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

Wiewiórka MS, Messina A, Pacholewska A, Maffioletti S, Gawrysiak P, Okoniewski MJ.

Bioinformatics. 2014 Sep 15;30(18):2652-3. doi: 10.1093/bioinformatics/btu343. Epub 2014 May 19.

PMID:
24845651
4.

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.

Nguyen T, Shi W, Ruden D.

BMC Res Notes. 2011 Jun 6;4:171. doi: 10.1186/1756-0500-4-171.

5.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.

Schumacher A, Pireddu L, Niemenmaa M, Kallio A, Korpelainen E, Zanetti G, Heljanko K.

Bioinformatics. 2014 Jan 1;30(1):119-20. doi: 10.1093/bioinformatics/btt601. Epub 2013 Oct 22.

6.

BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

Jácome AG, Fdez-Riverola F, Lourenço A.

Comput Methods Programs Biomed. 2016 Jul;131:63-77. doi: 10.1016/j.cmpb.2016.03.030. Epub 2016 Apr 8.

PMID:
27265049
7.

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

Taylor RC.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S1. doi: 10.1186/1471-2105-11-S12-S1.

8.

cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud.

Hodor P, Chawla A, Clark A, Neal L.

Bioinformatics. 2016 Jan 15;32(2):301-3. doi: 10.1093/bioinformatics/btv553. Epub 2015 Oct 1.

9.

HBLAST: Parallelised sequence similarity--A Hadoop MapReducable basic local alignment search tool.

O'Driscoll A, Belogrudov V, Carroll J, Kropp K, Walsh P, Ghazal P, Sleator RD.

J Biomed Inform. 2015 Apr;54:58-64. doi: 10.1016/j.jbi.2015.01.008. Epub 2015 Jan 24.

10.

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.

Niemenmaa M, Kallio A, Schumacher A, Klemelä P, Korpelainen E, Heljanko K.

Bioinformatics. 2012 Mar 15;28(6):876-7. doi: 10.1093/bioinformatics/bts054. Epub 2012 Feb 2.

11.

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.

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14.

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.

15.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.

16.

MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks.

Ohsumi TK, Borowsky ML.

Bioinformatics. 2012 Oct 1;28(19):2412-6. Epub 2012 Jul 19.

17.

GenomeView: a next-generation genome browser.

Abeel T, Van Parys T, Saeys Y, Galagan J, Van de Peer Y.

Nucleic Acids Res. 2012 Jan;40(2):e12. doi: 10.1093/nar/gkr995. Epub 2011 Nov 18.

18.

Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies.

Standish KA, Carland TM, Lockwood GK, Pfeiffer W, Tatineni M, Huang CC, Lamberth S, Cherkas Y, Brodmerkel C, Jaeger E, Smith L, Rajagopal G, Curran ME, Schork NJ.

BMC Bioinformatics. 2015 Sep 22;16:304. doi: 10.1186/s12859-015-0736-4.

19.

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA.

Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.

20.

MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization.

Zhou CL, Lam MW, Smith JR, Zemla AT, Dyer MD, Kuczmarski TA, Vitalis EA, Slezak TR.

BMC Bioinformatics. 2006 Oct 17;7:459.

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