Apr 142011
 

GeneSeq 1.0

:: DESCRIPTION

GeneSeq package provides methods to call SNP genotypes and infer haplotypes for a single individual given reads produced by whole-genome shotgun sequencing using high-throughput technologies such as 454, Illumina, and ABI SOLiD.  GeneSeq yields high genotype calling accuracy even from low read coverage by ecploting linkage disequilibrium patterns extracted from a reference panel such as those generated by the international Hapmap project.  Genotype and haplotype inference is  performed efficiently using a hierarchical factorial hidden Markov model (HF-HMM) integrating allele coverage information extracted from read data with haplotype frequencies inferred from the reference panel.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GeneSeq

:: MORE INFORMATION

J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu,
Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads,
BMC Bioinformatics 12(Suppl 1):S53, 2011

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