Long-read sequencing data analysis for yeasts

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

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

(2017) Sergey Koren et al.   GENOME RESEARCH

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

(2017) Jia-Xing Yue et al.   NATURE GENETICS

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

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

(2016) Heng Li   BIOINFORMATICS

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

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

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

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research

(2016) Sean J. McIlwain et al.   G3-Genes Genomes Genetics

The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen

(2015) Pooja K. Strope et al.   GENOME RESEARCH

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

(2015) Sara Goodwin et al.   GENOME RESEARCH

A population genomics insight into the Mediterranean origins of wine yeast domestication

(2015) Pedro Almeida et al.   MOLECULAR ECOLOGY

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

(2015) Robert VanBuren et al.   NATURE

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Ragout--a reference-assisted assembly tool for bacterial genomes

(2014) M. Kolmogorov et al.   BIOINFORMATICS

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes

(2014) Guénola Drillon et al.   PLoS One

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

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

A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

(2012) Estelle Proux-Wéra et al.   BMC BIOINFORMATICS

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Automated paleontology of repetitive DNA with REANNOTATE

(2008) Vini Pereira   BMC GENOMICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY