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

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

(2016) Heng Li   BIOINFORMATICS

Widespread Impact of Chromosomal Inversions on Gene Expression Uncovers Robustness via Phenotypic Buffering

(2016) Samina Naseeb et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

A hybrid approach for de novo human genome sequence assembly and phasing

(2016) Yulia Mostovoy et al.   NATURE METHODS

Population genomics of yeasts: towards a comprehensive view across a broad evolutionary scale

(2016) Jackson Peter et al.   YEAST

Population structure of mitochondrial genomes in Saccharomyces cerevisiae

(2015) John F. Wolters et al.   BMC GENOMICS

Genome assembly using Nanopore-guided long and error-free DNA reads

(2015) Mohammed-Amin Madoui et al.   BMC GENOMICS

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

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

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

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

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Successful test launch for nanopore sequencing

(2015) Nicholas J Loman et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Chromosomal Rearrangements as a Major Mechanism in the Onset of Reproductive Isolation in Saccharomyces cerevisiae

(2014) Jing Hou et al.   CURRENT BIOLOGY

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Decoding long nanopore sequencing reads of natural DNA

(2014) Andrew H Laszlo et al.   NATURE BIOTECHNOLOGY

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

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

A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

(2014) Joshua Quick et al.   GigaScience

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Genome-wide analysis of intraspecific transposon diversity in yeast

(2013) Claudine Bleykasten-Grosshans et al.   BMC GENOMICS

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

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

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

(2012) Elizabeth A Manrao et al.   NATURE BIOTECHNOLOGY

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies

(2011) M. C. Schatz et al.   BRIEFINGS IN BIOINFORMATICS

The Ty1 LTR-retrotransposon population in Saccharomyces cerevisiae genome: dynamics and sequence variations during mobility

(2011) Claudine Bleykasten-Grosshans et al.   FEMS YEAST RESEARCH

Adaptive seeds tame genomic sequence comparison

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li 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

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics