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

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Retraction Note to: Evaluation of next-generation sequencing software in mapping and assembly

(2011) SuYing Bao et al.   JOURNAL OF HUMAN GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Generalized Centroid Estimators in Bioinformatics

(2011) Michiaki Hamada et al.   PLoS One

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

GASSST: global alignment short sequence search tool

(2010) Guillaume Rizk et al.   BIOINFORMATICS

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

(2010) Michiaki Hamada et al.   BMC BIOINFORMATICS

De novo assembly of short sequence reads

(2010) K. Paszkiewicz et al.   BRIEFINGS IN BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Dindel: Accurate indel calls from short-read data

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

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Incorporating sequence quality data into alignment improves DNA read mapping

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

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA

(2010) Nils Homer et al.   GENOME BIOLOGY

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

(2009) Yangho Chen et al.   BIOINFORMATICS

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

SeqMap: mapping massive amount of oligonucleotides to the genome

(2008) H. Jiang et al.   BIOINFORMATICS

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Uncertainty in homology inferences: Assessing and improving genomic sequence alignment

(2007) G. Lunter et al.   GENOME RESEARCH