Genotype and SNP calling from next-generation sequencing data

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies

(2010) E. R. Martin et al.   BIOINFORMATICS

Design of association studies with pooled or un-pooled next-generation sequencing data

(2010) Su Yeon Kim et al.   GENETIC EPIDEMIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

(2010) Yingrui Li et al.   NATURE GENETICS

Intensity normalization improves color calling in SOLiD sequencing

(2010) Hao Wu et al.   NATURE METHODS

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

The Relationship between Imputation Error and Statistical Power in Genetic Association Studies in Diverse Populations

(2009) Lucy Huang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li 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

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

(2009) J. B. Li et al.   GENOME RESEARCH

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

(2009) W.-C. Kao et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Population genomics of domestic and wild yeasts

(2009) Gianni Liti et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Exome Sequencing of a Multigenerational Human Pedigree

(2009) Dale Hedges et al.   PLoS One

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

(2008) I. Hellmann et al.   GENOME RESEARCH

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

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

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE