GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

CONSERTING: integrating copy-number analysis with structural-variation detection

(2015) Xiang Chen et al.   NATURE METHODS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

Population-based structural variation discovery with Hydra-Multi

(2014) Michael R. Lindberg et al.   BIOINFORMATICS

Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads

(2014) Jan Schröder et al.   BIOINFORMATICS

The Architecture and Evolution of Cancer Neochromosomes

(2014) Dale W. Garsed et al.   CANCER CELL

Global optimization of somatic variant identification in cancer genomes with a global community challenge

(2014) Paul C Boutros et al.   NATURE GENETICS

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

SEQuel: improving the accuracy of genome assemblies

(2012) R. Ronen et al.   BIOINFORMATICS

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

(2011) Kim Wong et al.   GENOME BIOLOGY

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

(2010) Iman Hajirasouliha 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

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

(2009) Ken Chen et al.   NATURE METHODS

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE