A guide to sequence your favorite plant genomes

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

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

10KP: A phylodiverse genome sequencing plan

(2018) Shifeng Cheng et al.   GigaScience

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

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman 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

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

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

Is There an Upper Limit to Genome Size?

(2017) Oriane Hidalgo et al.   TRENDS IN PLANT SCIENCE

Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

(2017) Sebastian Reyes-Chin-Wo et al.   Nature Communications

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

(2017) Alex Harkess et al.   Nature Communications

Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage

(2017) Fay-Wei Li et al.   Database-The Journal of Biological Databases and Curation

A reference human genome dataset of the BGISEQ-500 sequencer

(2017) Jie Huang et al.   GigaScience

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

(2017) Sarah Siu Tze Mak et al.   GigaScience

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

(2017) Aleksey V Zimin et al.   GigaScience

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

(2016) Heng Li   BIOINFORMATICS

Sex and the Single Gametophyte: Revising the Homosporous Vascular Plant Life Cycle in Light of Contemporary Research

(2016) Christopher H. Haufler et al.   BIOSCIENCE

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

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

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

(2016) Helena Staňková et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome Mapping in Plant Comparative Genomics

(2016) Lindsay Chaney et al.   TRENDS IN PLANT SCIENCE

Draft genome of the living fossil Ginkgo biloba

(2016) Rui Guan et al.   GigaScience

Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads

(2015) S. Evan Staton et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

(2015) Robert VanBuren et al.   NATURE

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

The Norway spruce genome sequence and conifer genome evolution

(2013) Björn Nystedt et al.   NATURE

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Gaga, a New Fern Genus Segregated from Cheilanthes (Pteridaceae)

(2012) Fay-Wei Li et al.   SYSTEMATIC BOTANY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY

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

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