Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

Accurate viral population assembly from ultra-deep sequencing data

(2014) S. Mangul et al.   BIOINFORMATICS

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs

(2013) Haiyin Chen-Harris et al.   BMC GENOMICS

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

Observing micro-evolutionary processes of viral populations at multiple scales

(2013) R. J. Orton et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing

(2013) D. I. Lou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

(2012) John Archer et al.   BMC BIOINFORMATICS

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

Ultradeep Sequencing Analysis of Population Dynamics of Virus Escape Mutants in RNAi-Mediated Resistant Plants

(2012) Fernando Martínez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Massively Parallel Haplotyping on Microscopic Beads for the High-Throughput Phase Analysis of Single Molecules

(2012) Jérôme Boulanger et al.   PLoS One

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

(2012) Osvaldo Zagordi et al.   PLoS One

Comment on "Widespread RNA and DNA Sequence Differences in the Human Transcriptome"

(2012) W. Lin et al.   SCIENCE

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

(2012) Alexander R. Macalalad et al.   PLoS Computational Biology

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

A new approach for detecting low-level mutations in next-generation sequence data

(2012) Mingkun Li et al.   GENOME BIOLOGY

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

A simple method for the parallel deep sequencing of full influenza A genomes

(2011) Marie-Louise Kampmann et al.   JOURNAL OF VIROLOGICAL METHODS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Ultrasensitive detection of rare mutations using next-generation targeted resequencing

(2011) Patrick Flaherty et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Beyond the Consensus: Dissecting Within-Host Viral Population Diversity of Foot-and-Mouth Disease Virus by Using Next-Generation Genome Sequencing

(2010) C. F. Wright et al.   JOURNAL OF VIROLOGY

Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studies

(2010) R. Sanjuan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Adaptive approximate Bayesian computation

(2009) M. A. Beaumont et al.   BIOMETRIKA

Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes

(2009) Birgitte B. Simen et al.   JOURNAL OF INFECTIOUS DISEASES

Ultra‐Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse‐Transcriptase Inhibitor (NRTI)–Treated Patients and NRTI‐Naive Patients

(2009) Severine Margeridon‐Thermet et al.   JOURNAL OF INFECTIOUS DISEASES

Unequal distribution of RT-PCR artifacts along the E1–E2 region of Hepatitis C virus

(2009) Pilar Domingo-Calap et al.   JOURNAL OF VIROLOGICAL METHODS

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations

(2009) Gabriella Rozera et al.   Retrovirology

Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems

(2008) T. Toni et al.   Journal of the Royal Society Interface

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology