Graphtyper enables population-scale genotyping using pangenome graphs

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

(2016) Alexander T. Dilthey et al.   PLoS Computational Biology

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

Large-scale whole-genome sequencing of the Icelandic population

(2015) Daniel F Gudbjartsson et al.   NATURE GENETICS

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Genome alignment with graph data structures: a comparison

(2014) Birte Kehr et al.   BMC BIOINFORMATICS

Indexing Graphs for Path Queries with Applications in Genome Research

(2014) Jouni Siren et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Whole-genome sequence variation, population structure and demographic history of the Dutch population

(2014) Laurent C Francioli et al.   NATURE GENETICS

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Short read alignment with populations of genomes

(2013) L. Huang et al.   BIOINFORMATICS

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

(2013) Mengyao Zhao et al.   PLoS One

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

A population model for genotyping indels from next-generation sequence data

(2012) Haojing Shao et al.   NUCLEIC ACIDS RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Simultaneous alignment of short reads against multiple genomes

(2009) Korbinian Schneeberger et al.   GENOME BIOLOGY

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE