SvABA: genome-wide detection of structural variants and indels by local assembly

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

(2017) Xian Fan et al.   GENOME RESEARCH

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

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

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Chromothripsis from DNA damage in micronuclei

(2015) Cheng-Zhong Zhang et al.   NATURE

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

(2015) Peter H. Sudmant et al.   NATURE

Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes

(2015) Jiali Zhuang et al.   NUCLEIC ACIDS RESEARCH

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly

(2015) Rendong Yang et al.   Genome Medicine

Characterization of structural variants with single molecule and hybrid sequencing approaches

(2014) Anna Ritz et al.   BIOINFORMATICS

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping

(2014) Adam C English et al.   BMC BIOINFORMATICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Comprehensive variation discovery in single human genomes

(2014) Neil I Weisenfeld et al.   NATURE GENETICS

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

(2014) Giuseppe Narzisi et al.   NATURE METHODS

BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers

(2014) Ryan P. Abo et al.   NUCLEIC ACIDS RESEARCH

Characterization of HPV and host genome interactions in primary head and neck cancers

(2014) M. Parfenov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

TIGRA: A targeted iterative graph routing assembler for breakpoint assembly

(2013) K. Chen et al.   GENOME RESEARCH

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

(2012) Y. Drier et al.   GENOME RESEARCH

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration

(2012) Colby Chiang et al.   NATURE GENETICS

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

(2011) H. Li   BIOINFORMATICS

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

(2011) Philip J. Stephens et al.   CELL

Chromosome Catastrophes Involve Replication Mechanisms Generating Complex Genomic Rearrangements

(2011) Pengfei Liu et al.   CELL

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer

(2011) Geoff Fudenberg et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Small insertions and deletions (INDELs) in human genomes

(2010) J. M. Mullaney et al.   HUMAN MOLECULAR GENETICS

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Repair of ionizing radiation-induced DNA double-strand breaks by non-homologous end-joining

(2009) Brandi L. Mahaney et al.   BIOCHEMICAL JOURNAL

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

Gain-of-function mutations and copy number increases of Notch2 in diffuse large B-cell lymphoma

(2009) Suk-young Lee et al.   CANCER SCIENCE

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS