SVision: a deep learning approach to resolve complex structural variants

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

(2022) Jana Ebler et al.   NATURE GENETICS

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

(2021) Peter Ebert et al.   SCIENCE

Defining early changes in Alzheimer’s disease from RNA sequencing of brain regions differentially affected by pathology

(2021) Boris Guennewig et al.   Scientific Reports

Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer

(2021) Akihiro Fujimoto et al.   Genome Medicine

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

(2020) Sergey Aganezov et al.   GENOME RESEARCH

SVIM: Structural Variant Identification using Mapped Long Reads

(2019) David Heller et al.   BIOINFORMATICS

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Structural variation in the sequencing era

(2019) Steve S. Ho et al.   NATURE REVIEWS GENETICS

DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network

(2019) Lei Cai et al.   BMC BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

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

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

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

(2015) Peter H. Sudmant et al.   NATURE

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Characterizing complex structural variation in germline and somatic genomes

(2011) Aaron R. Quinlan et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS