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Cloudgene specifications


Unique identifier OMICS_04079
Name Cloudgene
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes


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Publication for Cloudgene

Cloudgene citations


Experiences with workflows for automating data intensive bioinformatics

Biol Direct
PMCID: 4539931
PMID: 26282399
DOI: 10.1186/s13062-015-0071-8

[…] s. An intensive cooperation with the research group Databases and Information Systems (DBIS) at the University of Innsbruck exists, developing data-intensive bioinformatics software solutions such as Cloudgene [], HaploGrep [] or the mtDNA-Server ( Lately, the developed workflow system Cloudgene has been utilized as the underlying architecture for the Michigan Imput […]


Validation of Next Generation Sequencing of Entire Mitochondrial Genomes and the Diversity of Mitochondrial DNA Mutations in Oral Squamous Cell Carcinoma

PLoS One
PMCID: 4532422
PMID: 26262956
DOI: 10.1371/journal.pone.0135643

[…] low cell on an Illumina HiSeq 2500 using 100-bp paired-end read chemistry.The paired-end fastq files from the Illumina HiSeq 2500 were analysed with our highly parallelized in-house-pipeline based on Cloudgene ([] and manuscript in preparation) called mtDNA-Server ( In a first step the data quality was controlled by creating reports in order to verify values such as […]


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

PMCID: 4455317
PMID: 26045962
DOI: 10.1186/s13742-015-0058-5

[…] to deliver bioinformatics pipelines on HPC and cloud resources. Galaxy provides a web-based graphical user interface (GUI) to bioinformatic programs, which simplifies the experience for the end user. CloudGene [] is a similar project that uses a GUI to help lower the learning curve for Hadoop adopters. In addition, CloudGene is specifically targeted at users in the life sciences. It uses a light-w […]


Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends

BioData Min
PMCID: 4224309
PMID: 25383096
DOI: 10.1186/1756-0381-7-22

[…] nodes. According to their results, MapReduce provides a substantial boost to the process.Cloudgene [] is a freely available platform to improve the usability of MapReduce programs in bioinformatics. Cloudgene is used to build a standardized graphical execution environment for currently available and future MapReduce programs, which can be integrated by using its plug-in interface. The results sho […]


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Cloudgene institution(s)
Division of Genetic Epidemiology, UT, USA

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