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SeqHBase specifications


Unique identifier OMICS_07580
Name SeqHBase
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Parallelization MapReduce
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes


No version available


  • person_outline Max He

Publication for SeqHBase

SeqHBase citations


Big Data Analytics for Genomic Medicine

Int J Mol Sci
PMCID: 5343946
PMID: 28212287
DOI: 10.3390/ijms18020412

[…] 6 ACMG genes is developed by Daneshjou et al. [], and a variant characterization framework for targeted analysis of relevant reads from high-throughput sequencing data is developed by Zhou et al. []. SeqHBase [] is a bioinformatics toolset for analyzing family-based WGS/WES data on a Big Data infrastructure. To deduce biological perceptions from large amounts of NGS data and inclusive clinical dat […]


Pathogenic Mutations in Cancer Predisposing Genes: A Survey of 300 Patients with Whole Genome Sequencing and Lifetime Electronic Health Records

PLoS One
PMCID: 5145192
PMID: 27930734
DOI: 10.1371/journal.pone.0167847

[…] c pathogenicity of germline mutations in 60 autosomal dominant cancer-predisposition genes () among 300 deceased patients at Marshfield Clinic with WGS data using an in-house analysis pipeline called SeqHBase [] based on the latest ACMG guidelines issued by the ACMG and the Association of for Molecular Pathology (AMP) []. Then we assessed clinical conditions for the patients who carried pathogenic […]


Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

PMCID: 4955563
PMID: 27195526
DOI: 10.1155/2016/3617572

[…] nes. To infer biological insights from massive amounts of NGS data and comprehensive clinical data in a short period of time, we have developed an analysis pipeline within a software framework called SeqHBase [] () to quickly identify disease- or drug-associated genetic variants. There were more than 27 million unique variants among 300 patients with WGS data that we analyzed using SeqHBase. In ad […]


Progress in oral personalized medicine: contribution of ‘omics’

PMCID: 4561229
PMID: 26344171
DOI: 10.3402/jom.v7.28223

[…] e, systems approaches to integrating and interpreting omics data will be necessary to fully harness the wealth of information that is being generated at unprecedented rates. Big Data toolsets such as SeqHBase ( with the capacity to analyze whole genome or exome sequencing data of 10 individuals in approximately 1 minute are being created and are essential to advancement […]


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SeqHBase institution(s)
Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA; Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA; Department of Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA; Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA; College of Science and Engineering, University of Minnesota-Twin Cities, MN, Minnesota, USA; Department of Medical Genetics Services, Marshfield Clinic, Marshfield, WI, USA; The Research Institute at Nationwide Children's Hospital, Columbus, OH,USA; Cold Spring Harbor Laboratory, Stanley Institute for Cognitive Genomics, Cold Spring Harbor, NY, USA; Utah Foundation for Biomedical Research, Provo, UT, USA; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA, USA; Department of Psychiatry, University of Southern California, Los Angeles, CA, USA

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