@INPROCEEDINGS{Halldorsson2011,
  author = {Halldorsson, Bjarni and Aguiar, Derek and Istrail, Sorin},
  title = {Haplotype phasing by multi-assembly of shared haplotypes: phase-dependent
	interactions between rare variants},
  booktitle = {Pac Symp Biocomput.},
  year = {2011},
  pages = {88--99},
  abstract = {In this paper we propose algorithmic strategies, Lander-Waterman-like
	statistical estimates, and genome-wide software for haplotype phasing
	by multi-assembly of shared haplotypes. Specifically, we consider
	four types of results which together provide a comprehensive workflow
	of GWAS data sets: (1) statistics of multi-assembly of shared haplotypes
	(2) graph theoretic algorithms for haplotype assembly based on conflict
	graphs of sequencing reads (3) inference of pedigree structure through
	haplotype sharing via tract finding algorithms and (4) multi-assembly
	of shared haplotypes of cases, controls, and trios. The input for
	the workflows that we consider are any of the combination of: (A)
	genotype data (B) next generation sequencing (NGS) (C) pedigree information.
	(1) We present Lander-Waterman-like statistics for NGS projects for
	the multi-assembly of shared haplotypes. Results are presented in
	Sec. 2. (2) In Sec. 3, we present algorithmic strategies for haplotype
	assembly using NGS, NGS + genotype data, and NGS + pedigree information.
	(3) This work builds on algorithms presented in Halldorsson et al.(1)
	and are part of the same library of tools co-developed for GWAS workflows.
	(4) Section 3.3.1 contains algorithmic strategies for multi-assembly
	of GWAS data. We present algorithms for assembling large data sets
	and for determining and using shared haplotypes to more reliably
	assemble and phase the data. Workflows 1-4 provide a set of rigorous
	algorithms which have the potential to identify phase-dependent interactions
	between rare variants in linkage equilibrium which are associated
	with cases. They build on our extensive work on haplotype phasing,(1-3)
	haplotype assembly,(4,5) and whole genome assembly comparison.(6).},
  doi = {citeulike-article-id:10540409},
  owner = {Derek},
  timestamp = {2012.05.08},
  url = {http://www.brown.edu/Research/Istrail_Lab/papers/9789814335058_0010.pdf},
  category = {Haplotype Assembly, Haplotype Analysis}
}