A draft human pangenome reference

Jasmine and Iris: population-scale structural variant comparison and analysis

(2023) Melanie Kirsche et al.   NATURE METHODS

Haplotype-aware pantranscriptome analyses using spliced pangenome graphs

(2023) Jonas A. Sibbesen et al.   NATURE METHODS

Gaps and complex structurally variant loci in phased genome assemblies

(2023) David Porubsky et al.   GENOME RESEARCH

Recombination between heterologous human acrocentric chromosomes

(2023) Andrea Guarracino et al.   NATURE

Increased mutation and gene conversion within human segmental duplications

(2023) Mitchell R. Vollger et al.   NATURE

Curated variation benchmarks for challenging medically relevant autosomal genes

(2022) Justin Wagner et al.   NATURE BIOTECHNOLOGY

ODGI: understanding pangenome graphs

(2022) Andrea Guarracino et al.   BIOINFORMATICS

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

(2022) Ting Wang et al.   NATURE

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

(2022) Jana Ebler et al.   NATURE GENETICS

Long-read mapping to repetitive reference sequences using Winnowmap2

(2022) Chirag Jain et al.   NATURE METHODS

Complete genomic and epigenetic maps of human centromeres

(2022) Nicolas Altemose et al.   SCIENCE

A complete reference genome improves analysis of human genetic variation

(2022) Sergey Aganezov et al.   SCIENCE

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Graph pangenome captures missing heritability and empowers tomato breeding

(2022) Yao Zhou et al.   NATURE

Genome evolution and diversity of wild and cultivated potatoes

(2022) Dié Tang et al.   NATURE

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

(2022) Erik Garrison et al.   PLoS Computational Biology

GBZ file format for pangenome graphs

(2022) Jouni Sirén et al.   BIOINFORMATICS

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

(2022) Marta Byrska-Bishop et al.   CELL

Semi-automated assembly of high-quality diploid human reference genomes

(2022) Erich D. Jarvis et al.   NATURE

Cyrius: accurate CYP2D6 genotyping using whole-genome sequencing data

(2021) Xiao Chen et al.   PHARMACOGENOMICS JOURNAL

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

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

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

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

(2021) Tsung-Yu Lu et al.   Nature Communications

Effective variant filtering and expected candidate variant yield in studies of rare human disease

(2021) Brent S. Pedersen et al.   npj Genomic Medicine

New strategies to improve minimap2 alignment accuracy

(2021) Heng Li   BIOINFORMATICS

Ensembl 2022

(2021) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

(2021) Jouni Sirén et al.   SCIENCE

Pangenome Graphs

(2020) Jordan M. Eizenga et al.   Annual Review of Genomics and Human Genetics

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Mapping and characterization of structural variation in 17,795 human genomes

(2020) Haley J. Abel et al.   NATURE

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Efficient dynamic variation graphs

(2020) Jordan M Eizenga et al.   BIOINFORMATICS

A diploid assembly-based benchmark for variants in the major histocompatibility complex

(2020) Chen-Shan Chin et al.   Nature Communications

Liftoff: accurate mapping of gene annotations

(2020) Alaina Shumate et al.   BIOINFORMATICS

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

(2020) Yan Gao et al.   BIOINFORMATICS

SVIM-asm: structural variant detection from haploid and diploid genome assemblies

(2020) David Heller et al.   BIOINFORMATICS

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

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

GENCODE 2021

(2020) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

SVIM: Structural Variant Identification using Mapped Long Reads

(2019) David Heller et al.   BIOINFORMATICS

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes

(2019) Ivar Grytten et al.   PLoS Computational Biology

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

Identifying centromeric satellites with dna-brnn

(2019) Heng Li   BIOINFORMATICS

svtools: population-scale analysis of structural variation

(2019) David E Larson et al.   BIOINFORMATICS

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

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

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

(2018) Ian T. Fiddes et al.   CELL

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

(2018) Ian T. Fiddes et al.   GENOME RESEARCH

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

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

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

The impact of structural variation on human gene expression

(2017) Colby Chiang et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

(2016) Kiana Mohajeri et al.   GENOME RESEARCH

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

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

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

(2015) Neil A. Miller et al.   Genome Medicine

ABRA: improved coding indel detection via assembly-based realignment

(2014) Lisle E. Mose et al.   BIOINFORMATICS

Low copy number of the salivary amylase gene predisposes to obesity

(2014) Mario Falchi et al.   NATURE GENETICS

Defining a personal, allele-specific, and single-molecule long-read transcriptome

(2014) Hagen Tilgner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HAL: a hierarchical format for storing and analyzing multiple genome alignments

(2013) Glenn Hickey et al.   BIOINFORMATICS

CGAL: computing genome assembly likelihoods

(2013) Atif Rahman et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative genomics: the bacterial pan-genome

(2008) Hervé Tettelin et al.   CURRENT OPINION IN MICROBIOLOGY