GeneSeq 1.0 – LD-based Genotype Calling from Shotgun Sequencing Reads

GeneSeq 1.0


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.


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


Command Line


  • Linux




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