Viral population analysis and minority-variant detection using short read next-generation sequencing

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Evolutionary Dynamics of Local Pandemic H1N1/2009 Influenza Virus Lineages Revealed by Whole-Genome Analysis

(2011) G. J. Baillie et al.   JOURNAL OF VIROLOGY

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing

(2011) Evelien M. Bunnik et al.   PLoS Pathogens

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Detection of low-frequency pretherapy chemokine (CXC motif) receptor 4 (CXCR4)-using HIV-1 with ultra-deep pyrosequencing

(2009) John Archer et al.   AIDS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation

(2008) Clinton H. Hansen et al.   PLoS Computational Biology