ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

(2014) Francesca Di Giallonardo et al.   NUCLEIC ACIDS RESEARCH

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model

(2013) Sandhya Prabhakaran et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Probabilistic Inference of Viral Quasispecies Subject to Recombination

(2013) Armin Töpfer et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Haplotype and minimum-chimerism consensus determination using short sequence data

(2012) Shawn T O'Neil et al.   BMC GENOMICS

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

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

Dynamics of Hepatitis B Virus Quasispecies in Association with Nucleos(t)ide Analogue Treatment Determined by Ultra-Deep Sequencing

(2012) Norihiro Nishijima et al.   PLoS One

Read length versus Depth of Coverage for Viral Quasispecies Reconstruction

(2012) Osvaldo Zagordi et al.   PLoS One

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

(2012) Niko Beerenwinkel et al.   Frontiers in Microbiology

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

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

Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing

(2011) Mattia CF Prosperi et al.   BMC 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

Ultra-deep sequencing for the analysis of viral populations

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

Assembly algorithms for next-generation sequencing data

(2010) Jason R. Miller et al.   GENOMICS

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

(2010) Osvaldo Zagordi et al.   NUCLEIC ACIDS RESEARCH

Quasispecies Theory and the Behavior of RNA Viruses

(2010) Adam S. Lauring et al.   PLoS Pathogens

The Feasibility of Using High Resolution Genome Sequencing of Influenza A Viruses to Detect Mixed Infections and Quasispecies

(2009) Muthannan A. Ramakrishnan et al.   PLoS One

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

Hepatitis B virus quasispecies susceptibility to entecavir confirms the relationship between genotypic resistance and patient virologic response

(2008) Carl J. Baldick et al.   JOURNAL OF HEPATOLOGY

A Bioinformatician's Guide to Metagenomics

(2008) V. Kunin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Viral Population Estimation Using Pyrosequencing

(2008) Nicholas Eriksson et al.   PLoS Computational Biology