Using state machines to model the Ion Torrent sequencing process and to improve read error rates

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

(2012) Kristof Beuf et al.   BMC BIOINFORMATICS

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

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

The battle for sequencing supremacy

(2012) Michael Eisenstein   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FAAST: Flow-space Assisted Alignment Search Tool

(2011) Fredrik Lysholm et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Base-calling for next-generation sequencing platforms

(2011) C. Ledergerber et al.   BRIEFINGS IN BIOINFORMATICS

Characteristics of 454 pyrosequencing data--enabling realistic simulation with flowsim

(2010) S. Balzer et al.   BIOINFORMATICS

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS