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High-throUghput GEnome SEQuencing HugeSeq

An automated pipeline for detecting genetic variants from high-throughput genome sequencing. HugeSeq is a fully integrated system for genome analysis from mapping reads to the identification and annotation of all types of variants: SNPS, Indels and SVs. The complete variant detection and characterization workflow of the HugeSeq pipeline is depicted below. The pipeline consists of a modular framework on which common algorithms are implemented. It is comprised of three phases: 1) a mapping phase that prepares, aligns and formats reads; 2) a sorting phase that combines and sort reads for parallel processing of variant calling; and 3) a reduction phase that calls and annotates the different variants (SNPs, Indels and SVs). HugeSeq is based on a MapReduce approach and runs in a parallel computational environment, making it highly efficient and scalable.

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HugeSeq classification

HugeSeq specifications

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Command line interface
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High performance computing:

HugeSeq distribution


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HugeSeq support


  • Hugo Y. K. Lam <>


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Department of Genetics, Stanford University, Stanford, CA, USA

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