Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing

‘At the crossroads towards polyploidy’: Genomic divergence and extent of homoploid hybridisation are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum , Compositae-Anthemideae)

(2019) Florian Wagner et al.   NEW PHYTOLOGIST

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Comparative genomic and phylogenetic analyses of Populus section Leuce using complete chloroplast genome sequences

(2019) Kai Gao et al.   Tree Genetics & Genomes

Long‐fragment targeted capture for long‐read sequencing of plastomes

(2019) Kevin Bethune et al.   Applications in Plant Sciences

Complete Chloroplast Genome of Pinus densiflora Siebold & Zucc. and Comparative Analysis with Five Pine Trees

(2019) Hye-In Kang et al.   Forests

Complete plastome of Leucanthemum maximum, the first in genus Leucanthemum

(2019) Haimei Chen et al.   Mitochondrial DNA Part B-Resources

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

GB2sequin - A file converter preparing custom GenBank files for database submission

(2018) Pascal Lehwark et al.   GENOMICS

Passiflora plastome sequencing reveals widespread genomic rearrangements

(2018) Samar O. Rabah et al.   Journal of Systematics and Evolution

Optimized Method of Extracting Rice Chloroplast DNA for High-Quality Plastome Resequencing and de Novo Assembly

(2018) Takeshi Takamatsu et al.   Frontiers in Plant Science

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Correcting palindromes in long reads after whole-genome amplification

(2018) Sven Warris et al.   BMC GENOMICS

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

(2018) Weiwen Wang et al.   BMC GENOMICS

Assembly of a Complete Mitogenome of Chrysanthemum nankingense Using Oxford Nanopore Long Reads and the Diversity and Evolution of Asteraceae Mitogenomes

(2018) Shuaibin Wang et al.   Genes

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

(2017) Sergey Koren et al.   GENOME RESEARCH

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

(2017) Rubén Sancho et al.   NEW PHYTOLOGIST

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

(2017) Shairul Izan et al.   Frontiers in Plant Science

Rapid de novo assembly of the European eel genome from nanopore sequencing reads

(2017) Hans J. Jansen et al.   Scientific Reports

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules

(2016) Jeremiah Wala et al.   BIOINFORMATICS

Strategies for complete plastid genome sequencing

(2016) Alex D. Twyford et al.   Molecular Ecology Resources

The Complete Chloroplast Genome Sequence of the Medicinal Plant Swertia mussotii Using the PacBio RS II Platform

(2016) Beibei Xiang et al.   MOLECULES

The Complete Chloroplast Genome Sequences for Four Amaranthus Species (Amaranthaceae)

(2016) Lindsay Chaney et al.   Applications in Plant Sciences

Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes

(2015) Joseph F. Walker et al.   AMERICAN JOURNAL OF BOTANY

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

(2015) David Laehnemann et al.   BRIEFINGS IN BIOINFORMATICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates

(2015) Andan Zhu et al.   NEW PHYTOLOGIST

Third generation sequencing: technology and its potential impact on evolutionary biodiversity research

(2015) Christoph Bleidorn   SYSTEMATICS AND BIODIVERSITY

PacBio Sequencing and Its Applications

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

Complete Chloroplast Genome of the Multifunctional Crop Globe Artichoke and Comparison with Other Asteraceae

(2015) Pasquale L. Curci et al.   PLoS One

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

(2014) Joey Shaw et al.   AMERICAN JOURNAL OF BOTANY

Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships

(2014) Hui Huang et al.   BMC EVOLUTIONARY BIOLOGY

Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants

(2014) Peter Civáň et al.   Genome Biology and Evolution

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

(2014) Cédric Mariac et al.   Molecular Ecology Resources

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

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

A Long PCR–Based Approach for DNA Enrichment Prior to Next-Generation Sequencing for Systematic Studies

(2014) Simon Uribe-Convers et al.   Applications in Plant Sciences

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Complete Chloroplast Genome Sequences of Mongolia Medicine Artemisia frigida and Phylogenetic Relationships with Other Plants

(2013) Yue Liu et al.   PLoS One

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

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

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

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The Complete Chloroplast Genome of 17 Individuals of Pest Species Jacobaea vulgaris: SNPs, Microsatellites and Barcoding Markers for Population and Phylogenetic Studies

(2011) L. Doorduin et al.   DNA RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Database indexing for production MegaBLAST searches

(2008) Aleksandr Morgulis et al.   BIOINFORMATICS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH