Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

A Genome-Wide Hybrid Incompatibility Landscape between Caenorhabditis briggsae and C. nigoni

(2015) Yu Bi et al.   PLoS Genetics

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

A Method for Rapid and Simultaneous Mapping of Genetic Loci and Introgression Sizes in Nematode Species

(2012) Cheung Yan et al.   PLoS One

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Whole Genome Sequencing Highlights Genetic Changes Associated with Laboratory Domestication of C. elegans

(2010) Katherine P. Weber et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes

(2009) A. Barriere et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Whole-genome sequencing and variant discovery in C. elegans

(2008) LaDeana W Hillier et al.   NATURE METHODS