HIVE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool HIVE

Tool usage distribution map

This map represents all the scientific publications referring to HIVE per scientific context
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Associated diseases

This word cloud represents HIVE usage per disease context

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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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