Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions

iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases

(2016) Yi Zheng et al.   Molecular Plant

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool

(2015) Jennifer M. Shelton et al.   BMC GENOMICS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

De novo and comparative transcriptome analysis of cultivated and wild spinach

(2015) Chenxi Xu et al.   Scientific Reports

Evidence for a Common Origin of Homomorphic and Heteromorphic Sex Chromosomes in Distinct Spinacia Species

(2015) Satoshi Fujito et al.   G3-Genes Genomes Genetics

Nitrate and oxalate in germplasm collections of spinach and other leafy vegetables

(2015) Svein Solberg et al.   Emirates Journal of Food and Agriculture

QuorUM: An Error Corrector for Illumina Reads

(2015) Guillaume Marçais et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

An analysis of genetic differentiation and geographical variation of spinach germplasm using SSR markers

(2013) Kouhei Kuwahara et al.   Plant Genetic Resources-Characterization and Utilization

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

(2012) Hiroaki Iwata et al.   NUCLEIC ACIDS RESEARCH

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Ruibang Luo et al.   GigaScience

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Natural Variation of Folate Content and Composition in Spinach (Spinacia oleracea) Germplasm

(2011) M. J. I. Shohag et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

Exploring Repetitive DNA Landscapes Using REPCLASS, a Tool That Automates the Classification of Transposable Elements in Eukaryotic Genomes

(2009) Cédric Feschotte et al.   Genome Biology and Evolution

The nature of selection during plant domestication

(2009) Michael D. Purugganan et al.   NATURE

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Characterization of a Resistance Locus (Pfs-1) to the Spinach Downy Mildew Pathogen (Peronospora farinosa f. sp. spinaciae) and Development of a Molecular Marker Linked to Pfs-1

(2008) B. M. Irish et al.   PHYTOPATHOLOGY