Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

Optimisation of DNA extraction and validation of PCR assays to detect Mycobacterium avium subsp. paratuberculosis

(2015) Verlaine J. Timms et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Completing bacterial genome assemblies: strategy and performance comparisons

(2015) Yu-Chieh Liao et al.   Scientific Reports

Adaptable probabilistic mapping of short reads using position specific scoring matrices

(2014) Peter Kerpedjiev et al.   BMC BIOINFORMATICS

Comparison of Genome Sequencing Technology and Assembly Methods for the Analysis of a GC-Rich Bacterial Genome

(2014) Derrick Scott et al.   CURRENT MICROBIOLOGY

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

(2014) Arthur W. Pightling et al.   PLoS One

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

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

Whole-Genome Sequencing for Rapid Susceptibility Testing of M. tuberculosis

(2013) Claudio U. Köser et al.   NEW ENGLAND JOURNAL OF MEDICINE

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

(2013) Midori Kato-Maeda et al.   PLoS One

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Whole Genome Sequencing Reveals Complex Evolution Patterns of Multidrug-Resistant Mycobacterium tuberculosis Beijing Strains in Patients

(2013) Matthias Merker et al.   PLoS One

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

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

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

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Accurate and comprehensive sequencing of personal genomes

(2011) S. S. Ajay et al.   GENOME RESEARCH

Whole-Genome Sequencing and Social-Network Analysis of a Tuberculosis Outbreak

(2011) Jennifer L. Gardy et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Interactive microbial genome visualization with GView

(2010) Aaron Petkau et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

(2009) Arnold Stein et al.   NUCLEIC ACIDS RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology