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

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

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

Inferring viral quasispecies spectra from 454 pyrosequencing reads

(2011) Irina Astrovskaya et al.   BMC 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

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

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

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Dynamics of HIV-1 Quasispecies during Antiviral Treatment Dissected Using Ultra-Deep Pyrosequencing

(2010) Charlotte Hedskog et al.   PLoS One

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

(2010) John Archer et al.   PLoS Computational Biology

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design

(2009) Valerie F. Boltz 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

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection

(2008) N. Malhis et al.   BIOINFORMATICS

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

(2008) W. Brockman et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

(2008) J. F. Salazar-Gonzalez et al.   JOURNAL OF VIROLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology