Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps

(2022) Mitchell R Vollger et al.   BIOINFORMATICS

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

(2022) Ren-Gang Zhang et al.   Horticulture Research

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families

(2022) Alessia Russo et al.   Frontiers in Plant Science

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

(2022) Erich D. Jarvis 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

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

(2021) Peng Qin et al.   CELL

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

(2021) Matthew B. Hufford et al.   SCIENCE

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

(2021) Bo Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The genetic and epigenetic landscape of the Arabidopsis centromeres

(2021) Matthew Naish et al.   SCIENCE

Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics

(2020) Wen-Biao Jiao et al.   Nature Communications

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

(2020) Shujun Ou et al.   Nature Communications

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

(2020) Sergey Nurk et al.   GENOME RESEARCH

A truncated singleton NLR causes hybrid necrosis in Arabidopsis thaliana

(2020) A Cristina Barragan et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2020) David Porubsky et al.   NATURE BIOTECHNOLOGY

Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore

(2020) Dandan Lang et al.   GigaScience

TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome

(2019) Weijia Su et al.   Molecular Plant

Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection

(2019) Jieming Shi et al.   PLANT PHYSIOLOGY

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set

(2019) Boas Pucker et al.   PLoS One

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

LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

(2019) Shujun Ou et al.   Mobile DNA

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Genetic and epigenetic variation in 5S ribosomal RNA genes reveals genome dynamics in Arabidopsis thaliana

(2018) Lauriane Simon et al.   NUCLEIC ACIDS RESEARCH

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

Long-read sequence and assembly of segmental duplications

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

A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

(2018) Stéphane Deschamps et al.   Nature Communications

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

(2017) Shamoni Maheshwari et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser 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

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana

(2017) Fernando A. Rabanal et al.   G3-Genes Genomes Genetics

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

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

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

Chromosome-level assembly ofArabidopsis thalianaLerreveals the extent of translocation and inversion polymorphisms

(2016) Luis Zapata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny

(2016) Boas Pucker et al.   PLoS One

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

The Split-Apply-Combine Strategy for Data Analysis

(2015) Hadley Wickham   Journal of Statistical Software

HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes

(2014) W. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long-read, whole-genome shotgun sequence data for five model organisms

(2014) Kristi E Kim et al.   Scientific Data

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

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

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

(2009) Thomas K. Wolfgruber et al.   PLoS Genetics

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE