Reducing assembly complexity of microbial genomes with single-molecule sequencing

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

(2013) Scott C. Clark et al.   BIOINFORMATICS

GAGE-B: an evaluation of genome assemblers for bacterial organisms

(2013) Tanja Magoc et al.   BIOINFORMATICS

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

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

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score

(2012) Hayan Lee et al.   BIOINFORMATICS

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

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

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

Phylogeny of Shiga Toxin-Producing Escherichia coli O157 Isolated from Cattle and Clinically Ill Humans

(2012) J. L. Bono et al.   MOLECULAR BIOLOGY AND EVOLUTION

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

A hybrid approach for the automated finishing of bacterial genomes

(2012) Ali Bashir et al.   NATURE BIOTECHNOLOGY

Reevaluating Assembly Evaluations with Feature Response Curves: GAGE and Assemblathons

(2012) Francesco Vezzi et al.   PLoS One

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

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

Diversity of Multidrug-ResistantSalmonella entericaStrains Associated with Cattle at Harvest in the United States

(2011) Dayna M. Brichta-Harhay et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

(2011) I. Pagani et al.   NUCLEIC ACIDS RESEARCH

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology

(2010) Thomas D. Otto et al.   BIOINFORMATICS

Assembly complexity of prokaryotic genomes using short reads

(2010) Carl Kingsford et al.   BMC BIOINFORMATICS

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing

(2009) Niranjan Nagarajan et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

(2008) T. Durfee et al.   JOURNAL OF BACTERIOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY