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A reliable big data-based computational toolset for efficiently manipulating genome-wide variants, annotations and every-site coverage in NGS studies. SeqHBase uses a heuristic framework of inheritance information for detecting de novo, inherited homozygous or compound heterozygous mutations that may be disease-contributing in trios, nuclear families and/or extended families. It shows very good performance on three different examples of family based sequencing data and is scalable by virtue of its basis on MapReduce framework.

Software type:
Framework
Interface:
Command line interface
Restrictions to use:
Academic users only
Operating system:
Unix/Linux
Parallelization:
MapReduce
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Max He <max.he at omicspace.org>
  • (He et al., 2015) SeqHBase: a big data toolset for family based sequencing data analysis. Journal of medical genetics.
    PMID: 25587064
  • (Mainzer et al., 2015) Isaac, the Illumina variant calling workflow. bioRxiv.
    DOI: 10.1101/031021
  • (Liu et al., 2013) Variant callers for next-generation sequencing data: a comparison study. PloS one.
    PMID: 24086590
  • (Nielsen et al., 2011) Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics.
    PMID: 21587300
  • (Altmann et al., 2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Human genetics.
    PMID: 22886560
  • (Pabinger et al., 2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics.
    PMID: 23341494
  • (Yi et al., 2014) Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids research.
    PMID: 24831545
  • (Pirooznia et al., 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human genomics.
    PMID: 25078893

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