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HIVE specifications


Unique identifier OMICS_11347
Alternative name High-performance Integrated Virtual Environment
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Database management system MySQL
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes


  • HIVE-heptagon
  • HIVE-hexagon aligner
  • HIVE-octagon
  • HIVE-seq


No version available


  • person_outline Vahan Simonyan

Publications for High-performance Integrated Virtual Environment

HIVE citations


Pressure for Pattern Specific Intertypic Recombination between Sabin Polioviruses: Evolutionary Implications

PMCID: 5707560
PMID: 29165333
DOI: 10.3390/v9110353

[…] 2495).Bioinformatic analysis was performed using two in-house software packages: ‘swarm’ program running on MacPro (Apple, Cuppertino, CA, USA) computers in UNIX (Darwin) environment, and cloud-based HIVE (highly-integrated virtual environment) system []. The analysis pipeline included the following steps. First, raw sequence data were pre-screened to eliminate low-quality reads and to remove adap […]


Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization

Sci Rep
PMCID: 5498541
PMID: 28680050
DOI: 10.1038/s41598-017-05088-4
call_split See protocol

[…] VE system. The alignments of the two sets of raw data were performed independently initially against the reference genome of L. infantum available on the genome database ( using the HIVE Hexagon aligner (Fig. ). In addition, we have also used Leishmania donovani wild type genome as a reference (provided by Dr. Peter Myler, Genbank accession number to be provided) in situations wh […]


Advancing Public Health Using Regulatory Science to Enhance Development and Regulation of Medical Products: Food and Drug Administration Research at the Center for Biologics Evaluation and Research

PMCID: 5466996
PMID: 28660187
DOI: 10.3389/fmed.2017.00071

[…] as digital X-ray, ultrasound, and a 4.7 T MRI.In addition, CBER developed hardware infrastructure and a bioinformatics team to support transfer, storage, and analysis of large, complex datasets. This high-performance integrated virtual environment (HIVE) supports analysis of NGS data generated not only by our own researchers but also provided by sponsors in regulatory submissions. In addition, CBE […]


Fast Dissemination of New HIV 1 CRF02/A1 Recombinants in Pakistan

PLoS One
PMCID: 5156399
PMID: 27973597
DOI: 10.1371/journal.pone.0167839
call_split See protocol

[…] licons and TruSeq libraries, respectively. The final consensus sequence from each library was obtained by assembling raw sequences reads using Geneious software (Biomatters, Auckland, New Zealand) or High-performance Integrated Virtual Environment (HIVE) [].The final sequences were aligned together with subtype reference sequences from HIV database in Los Alamos ( using CLUSTAL W […]


Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

PMCID: 4932478
PMID: 27110816
DOI: 10.3390/pharmaceutics8020015

[…] pping, variant calling and de novo genome assembly services (backed by AWS) []; DNANexus’s cloud service (also backed by AWS) with tools for ChiP-seq, RNA-seq, read mapping, and variant detection []; High-performance Integrated Virtual Environment (HIVE) with storage and various tools including reference based or de novo assembly services hosted on enterprise, appliance or cloud deployments []; Ga […]


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HIVE institution(s)
Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA; Department of Biochemistry and Molecular Biology, George Washington University Medical Center, WA, DC, USA
HIVE funding source(s)
Supported in part by the Food and Drug Administration Medical Countermeasures Initiative; by Medical Countermeasures Initiative and in part by R.M. research funds.

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