From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

Unrecognized sequence homologies may confound genome-wide association studies

(2012) Pierre Galichon et al.   NUCLEIC ACIDS RESEARCH

Heterogeneity and Tumor History

(2012) D. Shibata   SCIENCE

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

(2012) Andreas Keller et al.   Nature Communications

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Current Next Generation Sequencing technology may not meet forensic standards

(2011) Hans-Jürgen Bandelt et al.   Forensic Science International-Genetics

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Increased exonic de novo mutation rate in individuals with schizophrenia

(2011) Simon L Girard 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

A statistical method for the detection of variants from next-generation resequencing of DNA pools

(2010) V. Bansal   BIOINFORMATICS

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

SNP discovery performance of two second-generation sequencing platforms in the NOD2 gene region

(2010) Espen Melum et al.   HUMAN MUTATION

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

(2010) J. C. Roach et al.   SCIENCE

The Characterization of Twenty Sequenced Human Genomes

(2010) Kimberly Pelak et al.   PLoS Genetics

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

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

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

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

Evaluating length heteroplasmy in the human mitochondrial DNA control region

(2009) Lucy Forster et al.   INTERNATIONAL JOURNAL OF LEGAL MEDICINE

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

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

(2009) Martin Kircher et al.   GENOME BIOLOGY

Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation

(2008) Mannis van Oven et al.   HUMAN MUTATION

Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

(2008) Roger Horton et al.   IMMUNOGENETICS