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

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

(2011) Michiaki Hamada et al.   BIOINFORMATICS

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

Diverse somatic mutation patterns and pathway alterations in human cancers

(2010) Zhengyan Kan et al.   NATURE

Incorporating sequence quality data into alignment improves DNA read mapping

(2010) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

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

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS