GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface

Allele-Specific Genome-wide Profiling in Human Primary Erythroblasts Reveal Replication Program Organization

(2014) Rituparna Mukhopadhyay et al.   PLoS Genetics

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

(2012) C.-M. Liu et al.   BIOINFORMATICS

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

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

(2012) Brock A. Peters et al.   NATURE

GenPlay, a multipurpose genome analyzer and browser

(2011) Julien Lajugie et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence

(2011) Frederick E. Dewey et al.   PLoS Genetics

The Genomic HyperBrowser: inferential genomics at the sequence level

(2011) Geir K Sandve et al.   GENOME BIOLOGY

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Completely phased genome sequencing through chromosome sorting

(2010) H. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS