The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

(2020) Robert M. Waterhouse et al.   BMC BIOLOGY

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

BlobToolKit - Interactive Quality Assessment of Genome Assemblies

(2020) Richard Challis et al.   G3-Genes Genomes Genetics

Pangenome Graphs

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

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data

(2020) Vasanthan Jayakumar et al.   BMC GENOMICS

Building near-complete plant genomes

(2020) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

Chromosome‐level hybrid de novo genome assemblies as an attainable option for non‐model insects

(2020) Coline C. Jaworski et al.   Molecular Ecology Resources

A linked‐read approach to museomics: Higher quality de novo genome assemblies from degraded tissues

(2020) Jocelyn P. Colella et al.   Molecular Ecology Resources

A de novo chromosome‐level genome assembly of Coregonus sp. “ Balchen ”: One representative of the Swiss Alpine whitefish radiation

(2020) Rishi De‐Kayne et al.   Molecular Ecology Resources

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

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

(2020) Karen H. Miga et al.   NATURE

Massive haplotypes underlie ecotypic differentiation in sunflowers

(2020) Marco Todesco et al.   NATURE

Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)

(2020) James M. Pflug et al.   G3-Genes Genomes Genetics

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

(2020) Sergey Nurk et al.   GENOME RESEARCH

Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

(2020) Valentina Peona et al.   Molecular Ecology Resources

Chromosome-level genome assembly of a parent species of widely cultivated azaleas

(2020) Fu-Sheng Yang et al.   Nature Communications

Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

(2020) Julian Catchen et al.   G3-Genes Genomes Genetics

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

(2020) Eugenie C Yen et al.   GigaScience

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Understanding the Evolution of Reptile Chromosomes through Applications of Combined Cytogenetics and Genomics Approaches

(2019) Janine E. Deakin et al.   CYTOGENETIC AND GENOME RESEARCH

Errors in long-read assemblies can critically affect protein prediction

(2019) Mick Watson et al.   NATURE BIOTECHNOLOGY

Whole-genome resequencing of 472 Vitis accessions for grapevine diversity and demographic history analyses

(2019) Zhenchang Liang et al.   Nature Communications

Human contamination in bacterial genomes has created thousands of spurious proteins

(2019) Florian P. Breitwieser et al.   GENOME RESEARCH

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

(2019) Ou Wang et al.   GENOME RESEARCH

simuG: a general-purpose genome simulator

(2019) Jia-Xing Yue et al.   BIOINFORMATICS

Resolving repeat families with long reads

(2019) Philipp Bongartz   BMC BIOINFORMATICS

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

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

Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes

(2019) Hyungtaek Jung et al.   TRENDS IN PLANT SCIENCE

Chromosome‐level genome assembly of the predatorPropylea japonicato understand its tolerance to insecticides and high temperatures

(2019) Lijuan Zhang et al.   Molecular Ecology Resources

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

(2019) Ole K Tørresen et al.   NUCLEIC ACIDS RESEARCH

Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)

(2019) Gareth Linsmith et al.   GigaScience

Massive gene amplification on a recently formed Drosophila Y chromosome

(2019) Doris Bachtrog et al.   Nature Ecology & Evolution

Telomere length is repeatable, shortens with age and reproductive success, and predicts remaining lifespan in a long‐lived seabird

(2019) Coraline Bichet et al.   MOLECULAR ECOLOGY

Simulating Illumina Metagenomic Data with InSilicoSeq

(2018) Hadrien Gourlé et al.   BIOINFORMATICS

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Genetic and genomic monitoring with minimally invasive sampling methods

(2018) Emma L. Carroll et al.   Evolutionary Applications

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

A guide to sequence your favorite plant genomes

(2018) Fay-Wei Li et al.   Applications in Plant Sciences

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

(2018) Robert Lehmann et al.   Molecular Ecology Resources

How complete are “complete” genome assemblies?-An avian perspective

(2018) Valentina Peona et al.   Molecular Ecology Resources

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Mind the gaps: overlooking inaccessible regions confounds statistical testing in genome analysis

(2018) Diana Domanska et al.   BMC BIOINFORMATICS

Estimating the k-mer Coverage Frequencies in Genomic Datasets: A Comparative Assessment of the State-of-the-art

(2018) Swati C. Manekar et al.   CURRENT GENOMICS

Chromosome assembly of large and complex genomes using multiple references

(2018) Mikhail Kolmogorov et al.   GENOME RESEARCH

Improved reference genome of Aedes aegypti informs arbovirus vector control

(2018) Benjamin J. Matthews et al.   NATURE

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

New Approaches for Genome Assembly and Scaffolding

(2018) Edward S. Rice et al.   Annual Review of Animal Biosciences

Current Strategies of Polyploid Plant Genome Sequence Assembly

(2018) Maria Kyriakidou et al.   Frontiers in Plant Science

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Improved maize reference genome with single-molecule technologies

(2017) Yinping Jiao et al.   NATURE

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

(2009) Stefan Kurtz et al.   BMC GENOMICS

The role of repetitive DNA in structure and evolution of sex chromosomes in plants

(2009) E Kejnovsky et al.   HEREDITY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE