Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Curated variation benchmarks for challenging medically relevant autosomal genes

(2022) Justin Wagner et al.   NATURE BIOTECHNOLOGY

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

(2021) Xuefang Zhao et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The structure, function and evolution of a complete human chromosome 8

(2021) Glennis A. Logsdon et al.   NATURE

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

(2021) Jouni Sirén et al.   SCIENCE

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

Chromosome-scale, haplotype-resolved assembly of human genomes

(2020) Shilpa Garg et al.   NATURE BIOTECHNOLOGY

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

Fast and accurate genomic analyses using genome graphs

(2019) Goran Rakocevic et al.   NATURE GENETICS

HLA*LA—HLA typing from linearly projected graph alignments

(2019) Alexander T Dilthey et al.   BIOINFORMATICS

An open resource for accurately benchmarking small variant and reference calls

(2019) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs

(2019) Hannes P. Eggertsson et al.   Nature Communications

Integrating long-range connectivity information into de Bruijn graphs

(2018) Isaac Turner et al.   BIOINFORMATICS

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization

(2018) Maryam Ghareghani et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics

(2018) Chen Sun et al.   BIOINFORMATICS

Accurate genotyping across variant classes and lengths using variant graphs

(2018) Jonas Andreas Sibbesen et al.   NATURE GENETICS

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

A One-Penny Imputed Genome from Next-Generation Reference Panels

(2018) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Immune diversity sheds light on missing variation in worldwide genetic diversity panels

(2018) Laurent Abi-Rached et al.   PLoS One

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Graphtyper enables population-scale genotyping using pangenome graphs

(2017) Hannes P Eggertsson et al.   NATURE GENETICS

Genotype Imputation with Millions of Reference Samples

(2016) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast genotyping of known SNPs through approximatek-mer matching

(2016) Ariya Shajii et al.   BIOINFORMATICS

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

(2016) Dirk D. Dolle et al.   GENOME RESEARCH

Next-generation genotype imputation service and methods

(2016) Sayantan Das et al.   NATURE GENETICS

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

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

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble

(2015) Xiao Wang et al.   BMC BIOINFORMATICS

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

(2015) Peter H. Sudmant et al.   NATURE

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

Genome measures used for quality control are dependent on gene function and ancestry

(2014) Jing Wang et al.   BIOINFORMATICS

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

(2014) Andy Rimmer et al.   NATURE GENETICS

HLA Diversity in the 1000 Genomes Dataset

(2014) Pierre-Antoine Gourraud et al.   PLoS One

Three-stage quality control strategies for DNA re-sequencing data

(2013) Y. Guo et al.   BRIEFINGS IN BIOINFORMATICS

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold

(2012) Androniki Menelaou et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

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

(2012) Zamin Iqbal et al.   NATURE GENETICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

A linear complexity phasing method for thousands of genomes

(2011) Olivier Delaneau et al.   NATURE METHODS

High Frequencies of De Novo CNVs in Bipolar Disorder and Schizophrenia

(2011) Dheeraj Malhotra et al.   NEURON

Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism

(2011) Stephan J. Sanders et al.   NEURON

DNA-based methods in the immunohematology reference laboratory

(2011) Marion E. Reid et al.   TRANSFUSION AND APHERESIS SCIENCE

Genotype Imputation with Thousands of Genomes

(2011) Bryan Howie et al.   G3-Genes Genomes Genetics

Rare chromosomal deletions and duplications in attention-deficit hyperactivity disorder: a genome-wide analysis

(2010) Nigel M Williams et al.   LANCET

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

IPD—the Immuno Polymorphism Database

(2009) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Histo-Blood Group Gene Polymorphisms as Potential Genetic Modifiers of Infection and Cystic Fibrosis Lung Disease Severity

(2009) Jennifer L. Taylor-Cousar et al.   PLoS One

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia

(2008) T. Walsh et al.   SCIENCE

A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

(2008) David Melzer et al.   PLoS Genetics