Pangenome graph construction from genome alignments with Minigraph-Cactus

Recombination between heterologous human acrocentric chromosomes

(2023) Andrea Guarracino et al.   NATURE

A draft human pangenome reference

(2023) Wen-Wei Liao et al.   NATURE

Curated variation benchmarks for challenging medically relevant autosomal genes

(2022) Justin Wagner et al.   NATURE BIOTECHNOLOGY

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

(2022) Jana Ebler et al.   NATURE GENETICS

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

(2022) Alexander S. Leonard et al.   Nature Communications

Graph pangenome captures missing heritability and empowers tomato breeding

(2022) Yao Zhou et al.   NATURE

DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer

(2022) Gunjan Baid et al.   NATURE BIOTECHNOLOGY

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

The Need for a Human Pangenome Reference Sequence

(2021) Karen H. Miga et al.   Annual Review of Genomics and Human Genetics

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

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

(2020) Haley J. Abel et al.   NATURE

Efficient dynamic variation graphs

(2020) Jordan M Eizenga et al.   BIOINFORMATICS

Identification and Characterization of Breakpoints and Mutations on Drosophila melanogaster Balancer Chromosomes

(2020) Danny E. Miller et al.   G3-Genes Genomes Genetics

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

(2020) Yan Gao et al.   BIOINFORMATICS

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

Haplotype-aware graph indexes

(2019) Jouni Sirén et al.   BIOINFORMATICS

Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits

(2019) Mahul Chakraborty et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

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

Assembly of a pan-genome from deep sequencing of 910 humans of African descent

(2018) Rachel M. Sherman et al.   NATURE GENETICS

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

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

ABRA: improved coding indel detection via assembly-based realignment

(2014) Lisle E. Mose et al.   BIOINFORMATICS

Alignathon: a competitive assessment of whole-genome alignment methods

(2014) Dent Earl et al.   GENOME RESEARCH

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

(2014) W. Huang et al.   GENOME RESEARCH

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

(2013) Glenn Hickey et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Cactus Graphs for Genome Comparisons

(2011) Benedict Paten et al.   JOURNAL OF COMPUTATIONAL BIOLOGY