Use of a draft genome of coffee (Coffea arabica ) to identify SNPs associated with caffeine content

Variation in bean morphology and biochemical composition measured in different genetic groups of arabica coffee (Coffea arabica L.)

(2017) Hue T. M. Tran et al.   Tree Genetics & Genomes

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

(2016) Mohammed-Amin Madoui et al.   BMC BIOINFORMATICS

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols

(2016) Pedro J. Martínez-García et al.   PLANT JOURNAL

The Genome of a Southern Hemisphere Seagrass Species ( Zostera muelleri )

(2016) HueyTyng Lee et al.   PLANT PHYSIOLOGY

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus

(2016) Ahmed Sayadi et al.   PLoS One

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

Progress, challenges and the future of crop genomes

(2015) Todd P Michael et al.   CURRENT OPINION IN PLANT BIOLOGY

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

(2015) Gabriel R. A. Margarido et al.   PLoS Computational Biology

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species

(2014) Adam Healey et al.   Plant Methods

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

(2014) F. Denoeud et al.   SCIENCE

Get your high-quality low-cost genome sequence

(2014) Luigi Faino et al.   TRENDS IN PLANT SCIENCE

Mutated tumor alleles are expressed according to their DNA frequency

(2014) John C. Castle et al.   Scientific Reports

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt et al.   GENOME BIOLOGY

Draft genome sequence of the rubber tree Hevea brasiliensis

(2013) Ahmad Yamin Abdul Rahman et al.   BMC GENOMICS

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

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

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

(2012) Ruibang Luo et al.   GigaScience

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

(2011) Paul M. Magwene et al.   PLoS Computational Biology

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH