Variation graph toolkit improves read mapping by representing genetic variation in the reference

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

Graphtyper enables population-scale genotyping using pangenome graphs

(2017) Hannes P Eggertsson et al.   NATURE GENETICS

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

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

Biodiversity and distribution of polar freshwater DNA viruses

(2015) D. Aguirre de Carcer et al.   Science Advances

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

(2014) R. Durbin   BIOINFORMATICS

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

(2011) Michiaki Hamada et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

(2009) Bing Ge et al.   NATURE GENETICS