ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering

Prevalence and Evolution of Low Frequency HIV Drug Resistance Mutations Detected by Ultra Deep Sequencing in Patients Experiencing First Line Antiretroviral Therapy Failure

(2014) Marie-Anne Vandenhende et al.   PLoS One

V-Phaser 2: variant inference for viral populations

(2013) Xiao Yang et al.   BMC GENOMICS

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

(2012) Kristof Beuf et al.   BMC BIOINFORMATICS

Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes

(2012) M. Schirmer et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

ANALYSIS OF CONTEXT-DEPENDENT ERRORS FOR ILLUMINA SEQUENCING

(2012) IRINA ABNIZOVA et al.   Journal of Bioinformatics and Computational Biology

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data

(2011) Osvaldo Zagordi et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Hepatitis C virus resistance to protease inhibitors

(2011) Philippe Halfon et al.   JOURNAL OF HEPATOLOGY

New direct-acting antivirals' combination for the treatment of chronic hepatitis C

(2011) Tarik Asselah et al.   LIVER INTERNATIONAL

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Ultrasensitive detection of rare mutations using next-generation targeted resequencing

(2011) Patrick Flaherty et al.   NUCLEIC ACIDS RESEARCH

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

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