HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms

(2016) Anand Patel et al.   NUCLEIC ACIDS RESEARCH

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

MixSIH: a mixture model for single individual haplotyping

(2016) Hirotaka Matsumoto et al.   BMC GENOMICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

Probabilistic single-individual haplotyping

(2014) V. Kuleshov   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Inferring human population size and separation history from multiple genome sequences

(2014) Stephan Schiffels et al.   NATURE GENETICS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Whole-genome haplotyping approaches and genomic medicine

(2014) Gustavo Glusman et al.   Genome Medicine

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

(2014) Emily Berger et al.   PLoS Computational Biology

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Seeing is believing

(2013) Luc G Berthiaume   Nature Chemical Biology

Whole-genome haplotyping by dilution, amplification, and sequencing

(2013) F. Kaper et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the design of clone-based haplotyping

(2013) Christine Lo et al.   GENOME BIOLOGY

HapCompass: A Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data

(2012) Derek Aguiar et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Strobe sequence design for haplotype assembly

(2011) Christine Lo et al.   BMC BIOINFORMATICS

A comprehensively molecular haplotype-resolved genome of a European individual

(2011) E.-K. Suk et al.   GENOME RESEARCH

The importance of phase information for human genomics

(2011) Ryan Tewhey et al.   NATURE REVIEWS GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques

(2011) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

Optimal algorithms for haplotype assembly from whole-genome sequence data

(2010) D. He et al.   BIOINFORMATICS

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

HapCUT: an efficient and accurate algorithm for the haplotype assembly problem

(2008) V. Bansal et al.   BIOINFORMATICS

An MCMC algorithm for haplotype assembly from whole-genome sequence data

(2008) V. Bansal et al.   GENOME RESEARCH