Three-stage quality control strategies for DNA re-sequencing data

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

(2013) Yan Guo et al.   BIOINFORMATICS

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data

(2013) Qian Zhou et al.   PLoS One

Exome Sequencing Identifies PDE4D Mutations in Acrodysostosis

(2012) Hane Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exome Sequencing Identifies PDE4D Mutations as Another Cause of Acrodysostosis

(2012) Caroline Michot et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

Exome sequencing generates high quality data in non-target regions

(2012) Yan Guo et al.   BMC GENOMICS

The effect of strand bias in Illumina short-read sequencing data

(2012) Yan Guo et al.   BMC GENOMICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Combined immunodeficiency with life-threatening EBV-associated lymphoproliferative disorder in patients lacking functional CD27

(2012) E. Salzer et al.   HAEMATOLOGICA

The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation

(2012) Yan Guo et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Whole-exome sequencing detects somatic mutations of IDH1 in metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria (MC-HGA)

(2011) Lisenka E.L.M. Vissers et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Improving SNP discovery by base alignment quality

(2011) H. Li   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma

(2011) Sergey I Nikolaev et al.   NATURE GENETICS

Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia

(2011) Xiao-Jing Yan et al.   NATURE GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities

(2011) Matthew N Bainbridge et al.   GENOME BIOLOGY

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing

(2010) J. K. Teer et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

SHREC: a short-read error correction method

(2009) J. Schroder 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

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA