V-Phaser 2: variant inference for viral populations

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

De novo assembly of highly diverse viral populations

(2012) Xiao Yang 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

Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing

(2012) M. Lauck et al.   JOURNAL OF VIROLOGY

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

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

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

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

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

(2011) Osvaldo Zagordi 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

Ultra-deep sequencing for the analysis of viral populations

(2011) Niko Beerenwinkel et al.   Current Opinion in Virology

Intra- and Interhost Evolutionary Dynamics of Equine Influenza Virus

(2010) P. R. Murcia et al.   JOURNAL OF VIROLOGY

Whole-Genome Characterization of Human and Simian Immunodeficiency Virus Intrahost Diversity by Ultradeep Pyrosequencing

(2010) B. N. Bimber et al.   JOURNAL OF VIROLOGY

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

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology

(2010) Stephanie M. Willerth et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS