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HIVE-hexagon specifications


Unique identifier OMICS_12019
Name HIVE-hexagon
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability No
High performance computing Yes
Maintained No


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Publication for HIVE-hexagon

HIVE-hexagon citations


Complete Genome Sequence of a Nontypeable GII Norovirus Detected in Peru

Genome Announc
PMCID: 5843724
PMID: 29519825
DOI: 10.1128/genomeA.00095-18

[…] against the reference genomes (hu/pe/2013/gii.p24-gii.24/loreto1972, genbank accession number ky225989; and yuri, genbank accession number ab083780) to reconstruct a consensus sequence using the hive-hexagon (). a total of 635,163 reads were obtained, covering 7,465 nucleotides (nt) of the viral genome, with an average depth of coverage of 16,664× (range, 230 to 23,398×). the nucleotide […]


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

[…] identify taxonomical identity and the nearest reference neighbors. both sets of reads were aligned against leishmania infantum jpcm5 reference genome (retrieved from using hive-hexagon short read alignment algorithm. in certain cases, we have also used l. donovani genome as reference (provided by dr. peter myler) minimum alignment match length was chosen (120 […]


Chikungunya Virus as Cause of Febrile Illness Outbreak, Chiapas, Mexico, 2014

PMCID: 4622247
PMID: 26488312
DOI: 10.3201/eid2111.150546

[…] to be chikv negative if the sample was not positive by qrt-pcr or igm elisa., viral rna from 5 serum samples was sent for illumina deep sequencing and assembled by using the virus-specific hive-hexagon algorithm () and the ngen module in lasergene suite version 10 (bioinformatics pioneer dnastar, inc., madison, wi, usa ). single nucleotide polymorphisms were analyzed by using […]


Genetic Analysis of West Nile Virus Isolates from an Outbreak in Idaho, USA, 2006–2007

PMCID: 3799518
PMID: 24065039
DOI: 10.3390/ijerph10094486

[…] prevalence of transitions above transversions probably reflects the inherent bias of nucleotide misincorporation common to all known polymerases., the reads from each isolate were aligned by hive hexagon using ny99 (af196835) as the reference genome to perform snp and indel calls. snp calling results are shown in . illumina paired-end sequencing detected 70 mutations for isolate […]

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HIVE-hexagon institution(s)
Center for Biologics Evaluation and Research, US Food and Drug Administration, Chinakville, MD, USA; Department of Biochemistry and Molecular Biology, George Washington University Medical Center, WA, DC, USA; National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
HIVE-hexagon funding source(s)
This research was supported in part by the Food and Drug Administration Medical Countermeasures Initiative and in part by Intramural Research Program of the NIH, National Library of Medicine.

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