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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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Cloudgene citations


Experiences with workflows for automating data intensive bioinformatics

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

[…] systems like galaxy, chipster, and gpcr-modsim [], which we believe will enable us to reach a larger scientific community. we are experimenting with the workflow system luigi on our hpc system, and cloudgene [] on a previously established prototype hadoop cluster in a private cloud. for automating workflow execution we use either cron jobs and an external jenkins continuous integration […]


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

[…] 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 […]


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

[…] preprocessor for hadoop with better performance for splittable data files. for improved usability, we implemented a graphical user interface for crossbow in a private cloud environment using the cloudgene platform. all of the code and data in this study are freely available as open source in public repositories., from our experiments we can conclude that the improved hadoop pipeline scales […]

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

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