Making the difference: integrating structural variation detection tools (Q38287651)

1 September 2017

Making the difference: integrating structural variation detection tools (English)

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1 September 2017

Ke Lin

1

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1 September 2017

Sandra Smit

2

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1 September 2017

Guusje Bonnema

3

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1 September 2017

Gabino Sanchez-Perez

4

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1 September 2017

Dick de Ridder

5

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1 September 2017

language of work or name

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12 December 2014

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Briefings in Bioinformatics

1 September 2017

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1 September 2017

16

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1 September 2017

852-864

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1 September 2017

5

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Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.

1 September 2017

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

How and why chromosome inversions evolve

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Successive increases in the resistance of Drosophila to viral infection through a transposon insertion followed by a Duplication

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Molecular characterization of Rht-1 dwarfing genes in hexaploid wheat

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Gene transposition causing natural variation for growth in Arabidopsis thaliana

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

An integrated map of genetic variation from 1,092 human genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Whole-genome sequencing of multiple Arabidopsis thaliana populations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

DbVar and DGVa: public archives for genomic structural variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Effects of inversions on within- and between-species recombination and divergence

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Recombination load in a chromosomal inversion polymorphism of Drosophila subobscura

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Inversion variants in the human genome: role in disease and genome architecture

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Computational methods for discovering structural variation with next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Massively parallel sequencing approaches for characterization of structural variation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Mapping copy number variation by population-scale genome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome structural variation discovery and genotyping

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Paired-end mapping reveals extensive structural variation in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

TIGRA: a targeted iterative graph routing assembler for breakpoint assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

CLEVER: clique-enumerating variant finder

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Copy number variant detection in inbred strains from short read sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Accurate whole human genome sequencing using reversible terminator chemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Diverse mechanisms of somatic structural variations in human cancer genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Personalized copy number and segmental duplication maps using next-generation sequencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

An integrative probabilistic model for identification of structural variation in sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Detecting copy number variation with mated short reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

LUMPY: a probabilistic framework for structural variant discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Discovery and genotyping of genome structural polymorphism by sequencing on a population scale

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Efficient error correction for next-generation sequencing of viral amplicons

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Detecting and annotating genetic variations using the HugeSeq pipeline

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

A map of human genome variation from population-scale sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

A comprehensive map of mobile element insertion polymorphisms in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The standing pool of genomic structural variation in a natural population of Mimulus guttatus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Population structure and domestication revealed by high-depth resequencing of Korean cultivated and wild soybean genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Primate genome architecture influences structural variation mechanisms and functional consequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Tangram: a comprehensive toolbox for mobile element insertion detection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

RetroSeq: transposable element discovery from next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Using ERDS to infer copy-number variants in high-coverage genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

U87MG decoded: the genomic sequence of a cytogenetically aberrant human cancer cell line

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

forestSV: structural variant discovery through statistical learning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Sensitive and accurate detection of copy number variants using read depth of coverage

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Versatile and open software for comparing large genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome remodelling in a basal-like breast cancer metastasis and xenograft

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

SVM²: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Mapping and sequencing of structural variation from eight human genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Characterization of missing human genome sequences and copy-number polymorphic insertions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The diploid genome sequence of an individual human

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The complete genome of an individual by massively parallel DNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Whole-genome sequence variation, population structure and demographic history of the Dutch population

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome-wide variation within and between wild and domestic yak.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Strong signatures of selection in the domestic pig genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Nonhuman genetics. Strong male bias drives germline mutation in chimpanzees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Whole genome comparison of donor and cloned dogs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Deep resequencing reveals allelic variation in Sesamum indicum

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genome-wide genetic changes during modern breeding of maize

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Genomic evolution of Saccharomyces cerevisiae under Chinese rice wine fermentation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Within-host evolution of Staphylococcus aureus during asymptomatic carriage.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Simultaneous structural variation discovery among multiple paired-end sequenced genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

mrsFAST: a cache-oblivious algorithm for short-read mapping.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Accurate indel prediction using paired-end short reads

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

High-resolution human genome structure by single-molecule analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBU047

21 January 2018

Identifiers

DOI

10.1093/BIB/BBU047

1 reference

1 September 2017

journals/bib/LinSBSR15

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference