The effect of next-generation sequencing technology on complex trait research

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

(2010) James R. Lupski et al.   NEW ENGLAND JOURNAL OF MEDICINE

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

STATISTICAL COMPARISON OF METHODS TO ESTIMATE THE ERROR PROBABILITY IN SHORT-READ ILLUMINA SEQUENCING

(2010) IRINA ABNIZOVA et al.   Journal of Bioinformatics and Computational Biology

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

An evaluation of statistical approaches to rare variant analysis in genetic association studies

(2009) Andrew P. Morris et al.   GENETIC EPIDEMIOLOGY

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing

(2009) Murim Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes

(2009) S. Nejentsev et al.   SCIENCE

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic

(2009) Bo Eskerod Madsen et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Methods for Detecting Associations with Rare Variants for Common Diseases: Application to Analysis of Sequence Data

(2008) Bingshan Li et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

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

(2008) H. Li et al.   GENOME RESEARCH

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS