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

CLEVER: clique-enumerating variant finder

(2012) Tobias Marschall et al.   BIOINFORMATICS

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

(2012) Yue Jiang et al.   BIOINFORMATICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

(2011) Shin Suzuki et al.   BMC BIOINFORMATICS

Estimation of rearrangement phylogeny for cancer genomes

(2011) C. D. Greenman 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

Detection of structural variants and indels within exome data

(2011) Emre Karakoc et al.   NATURE METHODS

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

(2011) Jianmin Wang et al.   NATURE METHODS

ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads

(2011) Christopher A. Miller et al.   PLoS One

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE

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

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

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

(2008) Peter J Campbell et al.   NATURE GENETICS