CLEVER: clique-enumerating variant finder

Natural genetic variation caused by small insertions and deletions in the human genome

(2011) R. E. Mills et al.   GENOME RESEARCH

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan 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

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

(2009) Andy Itsara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions

(2009) Seunghak Lee et al.   NATURE METHODS

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

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

(2008) H. Li et al.   GENOME RESEARCH

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

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE