HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

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

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

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

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

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

Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads

(2019) Mitchell R. Vollger et al.   ANNALS OF HUMAN GENETICS

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Alpha satellite DNA biology: finding function in the recesses of the genome

(2018) Shannon M. McNulty et al.   CHROMOSOME RESEARCH

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Long-read sequence and assembly of segmental duplications

(2018) Mitchell R. Vollger et al.   NATURE METHODS

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

α satellite DNA variation and function of the human centromere

(2017) Lori L. Sullivan et al.   Nucleus

α satellite DNA variation and function of the human centromere

(2017) Lori L. Sullivan et al.   Nucleus

Icarus: visualizer for de novo assembly evaluation

(2016) Alla Mikheenko et al.   BIOINFORMATICS

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

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

(2016) Kiana Mohajeri et al.   GENOME RESEARCH

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

The Yin and Yang of Human Beta-Defensins in Health and Disease

(2012) Aaron Weinberg et al.   Frontiers in Immunology

Bambus 2: scaffolding metagenomes

(2011) Sergey Koren et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21

(2010) Nathalie Pironon et al.   BMC GENOMICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Allelic recombination between distinct genomic locations generates copy number diversity in human β-defensins

(2009) Suhaili Abu Bakar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH