Comparison of long-read methods for sequencing and assembly of a plant genome

Long-read human genome sequencing and its applications

(2020) Glennis A. Logsdon et al.   NATURE REVIEWS GENETICS

Chromosome-Scale Assembly and Annotation of the Macadamia Genome (Macadamia integrifolia HAES 741)

(2020) Catherine J. Nock et al.   G3-Genes Genomes Genetics

TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

(2020) Mengyang Xu et al.   GigaScience

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

(2019) Sarah Kingan et al.   Genes

A critical comparison of technologies for a plant genome sequencing project

(2019) Pirita Paajanen et al.   GigaScience

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

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Modern technologies and algorithms for scaffolding assembled genomes

(2019) Jay Ghurye et al.   PLoS Computational Biology

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

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

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

Innovations in plant genetics adapting agriculture to climate change

(2019) Robert J Henry   CURRENT OPINION IN PLANT BIOLOGY

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

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA

(2018) Lin Wang et al.   DNA RESEARCH

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld 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

Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae)

(2016) Catherine J. Nock et al.   BMC GENOMICS

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

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

Real-time selective sequencing using nanopore technology

(2016) Matthew Loose et al.   NATURE METHODS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Global agricultural intensification during climate change: a role for genomics

(2015) Michael Abberton et al.   PLANT BIOTECHNOLOGY JOURNAL

Genomics of crop wild relatives: expanding the gene pool for crop improvement

(2015) Marta Brozynska et al.   PLANT BIOTECHNOLOGY JOURNAL

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS