Accurate detection of complex structural variations using single-molecule sequencing

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

(2017) Martha Imprialou et al.   GENETICS

Long-read genome sequencing identifies causal structural variation in a Mendelian disease

(2017) Jason D Merker et al.   GENETICS IN MEDICINE

Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin

(2017) Stefan Dennenmoser et al.   MOLECULAR ECOLOGY

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits

(2017) Martha Imprialou et al.   GENETICS

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Mechanisms underlying structural variant formation in genomic disorders

(2016) Claudia M. B. Carvalho et al.   NATURE REVIEWS GENETICS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Sequencing Structural Variants in Cancer for Precision Therapeutics

(2016) Geoff Macintyre et al.   TRENDS IN GENETICS

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

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

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Structural variation mutagenesis of the human genome: Impact on disease and evolution

(2015) James R. Lupski   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

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

(2015) Peter H. Sudmant et al.   NATURE

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

(2014) Adam C English et al.   BMC BIOINFORMATICS

Exome sequence read depth methods for identifying copy number changes

(2014) L. Kadalayil et al.   BRIEFINGS IN BIOINFORMATICS

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

On the Power and the Systematic Biases of the Detection of Chromosomal Inversions by Paired-End Genome Sequencing

(2014) José Ignacio Lucas Lledó et al.   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Phenotypic impact of genomic structural variation: insights from and for human disease

(2013) Joachim Weischenfeldt et al.   NATURE REVIEWS GENETICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

Statistical challenges associated with detecting copy number variations with next-generation sequencing

(2012) Shu Mei Teo et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Low-copy repeats at the human VIPR2 gene predispose to recurrent and nonrecurrent rearrangements

(2012) Silvana Beri et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Pelizaeus-Merzbacher disease caused by a duplication-inverted triplication-duplication in chromosomal segments including the PLP1 region

(2012) Keiko Shimojima et al.   European Journal of Medical Genetics

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

(2012) T. Zichner et al.   GENOME RESEARCH

Evidence of novel fine-scale structural variation at autism spectrum disorder candidate loci

(2012) Dale J Hedges et al.   Molecular Autism

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Inverted genomic segments and complex triplication rearrangements are mediated by inverted repeats in the human genome

(2011) Claudia M B Carvalho et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS