Advances of next generation sequencing technologies and availability of short read data enable the detection of structural variations (SVs). Deletions, an important type of SVs, have been suggested in association with genetic diseases. There are three types of deletions: blunt…
Desktop app
G T A T C G C T A Platypus Platypus

Platypus

A tool designed for efficient and accurate variant-detection in high-throughput…

A tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high…

Desktop app
G T A T C G C T A BreakDancer BreakDancer

BreakDancer

A Perl/C++ package that provides genome-wide detection of structural variants…

A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancer sensitively and accurately detected indels ranging from 10…

Desktop app
G T A T C G C T A Cortex Cortex

Cortex

A tool for genome assembly and variation analysis from sequence data. You can…

A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples,…

Web app
G T A T C G C T A Clipping REveals… Clipping REveals STructure

CREST Clipping REveals STructure

An algorithm using NGS reads with partial alignments to a reference genome to…

An algorithm using NGS reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level. Application of CREST to whole-genome sequencing data from…

Desktop app
G T A T C G C T A Control-FREEC Control-FREEC

Control-FREEC

A tool for detection of copy-number changes and allelic imbalances (including…

A tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. Control-FREEC automatically computes, normalizes, segments copy number and beta allele…

Desktop app
G T A T C G C T A CNVnator CNVnator

CNVnator

An approach to discover, genotype, and characterize typical and atypical CNVs…

An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Overall, for CNVs accessible by RD, CNVnator has high sensitivity…

Desktop app
G T A T C G C T A RDXplorer RDXplorer

RDXplorer

A computational tool for copy number variants (CNV) detection in whole human…

A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm. The…

Desktop app
G T A T C G C T A Pindel Pindel

Pindel

Detects breakpoints of large deletions, medium sized insertions, inversions,…

Detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequence data. Pindel…

Desktop app
G T A T C G C T A PEMer PEMer

PEMer

A computational framework with simulation-based error models for inferring…

A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. The package is composed of three modules, PEMer…

Desktop app
G T A T C G C T A CNVer CNVer

CNVer

A method for CNV detection that supplements the depth-of-coverage with…

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of…

Desktop app
G T A T C G C T A DELLY DELLY

DELLY

An integrated structural variant prediction method that can detect deletions,…

An integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel…

Desktop app
G T A T C G C T A Copy number… Copy number estimation by a Mixture Of PoissonS

cn.MOPS Copy number estimation by a Mixture Of PoissonS

A data processing pipeline for copy number variations and aberrations (CNVs and…

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count…

Desktop app
G T A T C G C T A GASVPro GASVPro

GASVPro

Combines read depth information along with discordant paired-read mappings into…

Combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation.

Desktop app
G T A T C G C T A VariationHunter VariationHunter

VariationHunter

A tool for discovery of structural variation in one or more individuals…

A tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. VariationHunter is now capable of resolving incompatible SV calls through a…

Desktop app
G T A T C G C T A CNV-seq CNV-seq

CNV-seq

A method to detect copy number variation using shotgun sequencing. The method…

A method to detect copy number variation using shotgun sequencing. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of…

Desktop app
G T A T C G C T A SVDetect SVDetect

SVDetect

A tool to detect genomic structural variations from paired-end and mate-pair…

A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.

Desktop app
G T A T C G C T A Geometric Analysis of… Geometric Analysis of Structural Variants

GASV Geometric Analysis of Structural Variants

A tool for identifying structural variants (SVs) from paired-end sequencing…

A tool for identifying structural variants (SVs) from paired-end sequencing data. GASV is a geometric approach for identification, classification and comparison of structural variants. This approach…

Desktop app
G T A T C G C T A inGAP-sv inGAP-sv

inGAP-sv

Detects and visualizes structural variation from paired-end mapping data. Under…

Detects and visualizes structural variation from paired-end mapping data. Under this scheme, abnormally mapped read pairs are clustered based on the location of a gap signature. Several important…

Desktop app
G T A T C G C T A JointSLM JointSLM

JointSLM

An algorithm that extend the univariate SLM to the multivariate case in order…

An algorithm that extend the univariate SLM to the multivariate case in order to detect recurrent shifts in the mean of multiple sequential processes. The resolution of JointSLM strictly depends on…

Desktop app
G T A T C G C T A Clippers Clippers

Clippers

A program designed to identify long deletions of a genome as well as the RNA…

A program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads.

Desktop app
G T A T C G C T A readDepth readDepth

readDepth

This package for R can detect copy number aberrations by measuring the depth of…

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In contrast to other published methods, readDepth…

Desktop app
G T A T C G C T A AGE AGE

AGE

An algorithm for the correct alignment of two nucleotide sequences containing…

An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e. deletion, insertion, tandem duplication or inversion. The algorithm does not require the adjustment or…

Desktop app
G T A T C G C T A cnvHiTSeq cnvHiTSeq

cnvHiTSeq

A set of Java-based command-line tools for detecting Copy Number Variants…

A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.

Desktop app
G T A T C G C T A Mendelian-inheritance-AtTEntive…

MATE-CLEVER Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder

An approach that accurately discovers and genotypes indels longer than 30 bp…

An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios or…

Desktop app
G T A T C G C T A SoftSearch SoftSearch

SoftSearch

A sensitive structural variant (SV) detection tool for Illumina paired-end…

A sensitive structural variant (SV) detection tool for Illumina paired-end next-generation sequencing data.

Desktop app
G T A T C G C T A SVseq SVseq

SVseq

An improved approach for accurate and efficient calling of structural…

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.

Desktop app
G T A T C G C T A clipcrop clipcrop

clipcrop

A tool for detecting structural variations with single-base resolution using…

A tool for detecting structural variations with single-base resolution using soft-clipping information.

Desktop app
G T A T C G C T A SVMiner SVMiner

SVMiner

A model-based clustering method for genomic structural variant prediction and…

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

Desktop app
G T A T C G C T A PSSV PSSV

PSSV

A probabilistic method for somatic structural variation (SV) prediction by…

A probabilistic method for somatic structural variation (SV) prediction by jointly modeling discordant and concordant read counts. PSSV is specifically designed to predict somatic deletions,…

Desktop app
G T A T C G C T A Statistical… Statistical Structural Variant Analysis for NGS

SWAN Statistical Structural Variant Analysis for NGS

A statistical framework and algorithm for structural variant (SV) detection…

A statistical framework and algorithm for structural variant (SV) detection from whole genome sequencing data. SWAN integrates multiple features, including insert size, hanging read pairs and read…

Desktop app
G T A T C G C T A VarDict VarDict

VarDict

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict…

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict contains many features that are distinct from other variant callers, including linear performance to depth, intrinsic local…

Desktop app
G T A T C G C T A Manta Manta

Manta

Calls structural variants (SVs) and indels from mapped paired-end sequencing…

Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and…

Desktop app
G T A T C G C T A BreaKmer BreaKmer

BreaKmer

An approach that uses a 'kmer' strategy to assemble misaligned…

An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair…

Desktop app
G T A T C G C T A DeF-GPU DeF-GPU

DeF-GPU

A graphics processing unit (GPU)-based data mining method. DeF-GPU efficiently…

A graphics processing unit (GPU)-based data mining method. DeF-GPU efficiently and precisely identifies Hepatitis B viral (HBV) deletions from large NGS data, which generally contain millions of…

Desktop app
G T A T C G C T A Structural Variation… Structural Variation detection by STAck and Tail

SV-STAT Structural Variation detection by STAck and Tail

A statistical tool to quantify evidence for structural variation in genomic…

A statistical tool to quantify evidence for structural variation in genomic regions suspected of harboring rearrangements. SV-STAT extends existing methods by adjusting a chimeric read’s support of…

Desktop app
G T A T C G C T A Maximal Unique… Maximal Unique Matchdex

MUMdex Maximal Unique Matchdex

A package for aligning sequences to a reference genome. MUMdex consists of an…

A package for aligning sequences to a reference genome. MUMdex consists of an aligner, an alignment format, an analysis software and a portable population database of common structural variants to…

Desktop app
G T A T C G C T A Sprites Sprites

Sprites

Finds deletions from sequencing data. Sprites aligns a whole soft-clipping read…

Finds deletions from sequencing data. Sprites aligns a whole soft-clipping read rather than its clipped part to the target sequence, a segment of the reference which is determined by spanning reads,…

Desktop app
G T A T C G C T A COSMOS COSMOS

COSMOS

An accurate structural variation (SV) detection method, which compares the…

An accurate structural variation (SV) detection method, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner.…

Desktop app
G T A T C G C T A SVClassify SVClassify

SVClassify

Calculates annotations from one or more aligned bam files from many…

Calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate structural…

Desktop app
G T A T C G C T A TrioCNV TrioCNV

TrioCNV

A tool designed to jointly detecting copy number variations (CNVs) from whole…

A tool designed to jointly detecting copy number variations (CNVs) from whole genome sequencing data in parent-offspring trios. TrioCNV models read depth signal with the negative binomial regression…

Desktop app
G T A T C G C T A SV-Bay SV-Bay

SV-Bay

Detects structural variants in cancer using whole genome sequencing data with…

Detects structural variants in cancer using whole genome sequencing data with or without matched normal control sample. SV-Bay does not only use information about abnormal read mappings but also…

Desktop app
G T A T C G C T A PBHoney PBHoney

PBHoney

Considers both intra-read discordance and soft-clipped tails of long reads…

Considers both intra-read discordance and soft-clipped tails of long reads (>10,000 bp) to identify structural variants. As a proof of concept, we identify four structural variants and two genomic…

Desktop app
G T A T C G C T A FermiKit FermiKit

FermiKit

A variant calling pipeline for Illumina whole-genome germline data. It de novo…

A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions…

Desktop app
G T A T C G C T A Repeat Repeat

Repeat

Allows the repeat-aware and error-tolerant comparison of deletion predictions…

Allows the repeat-aware and error-tolerant comparison of deletion predictions given in VCF or BED format. Repeat operates at negligible false discovery rates. Thereby, it outperforms ad-hoc criteria,…

Desktop app
G T A T C G C T A MetaSV MetaSV

MetaSV

An integrated structural variation (SV) caller which leverages multiple…

An integrated structural variation (SV) caller which leverages multiple orthogonal SV signals for high accuracy and resolution. MetaSV proceeds by merging SVs from multiple tools for all types of…

Desktop app
G T A T C G C T A ReAd Pair spliT… ReAd Pair spliT Read-Structural Variant

RAPTR-SV ReAd Pair spliT Read-Structural Variant

A program designed to process previously aligned, Illumina Paired-end whole…

A program designed to process previously aligned, Illumina Paired-end whole genome sequence data to identify structural variants such as deletions, insertions and tandem duplications. Simulations…

Desktop app
G T A T C G C T A Copy Numbers Of Genes… Copy Numbers Of Genes in prokaryotes

CNOGpro Copy Numbers Of Genes in prokaryotes

Methods for assigning copy number states and breakpoints in resequencing…

Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms. CNOGpro will in some cases represent a significant jump in accuracy from other current…

Web app
G T A T C G C T A ViVar ViVar

ViVar

A comprehensive analysis platform for the processing, analysis and…

A comprehensive analysis platform for the processing, analysis and visualization of structural variation based on sequencing data or genomic microarrays, enabling the rapid identification of disease…

Desktop app
G T A T C G C T A Sample Heterogeneity… Sample Heterogeneity Estimation and Assembly by…

SHEAR Sample Heterogeneity Estimation and Assembly by Reference

A tool for next-generation sequencing data analysis that predicts SVs, accounts…

A tool for next-generation sequencing data analysis that predicts SVs, accounts for heterogeneous variants by estimating their representative percentages, and generates personal genomic sequences to…

Desktop app
G T A T C G C T A CLEVER CLEVER

CLEVER

An internal segment size based approach, which organizes all, including…

An internal segment size based approach, which organizes all, including concordant, reads into a read alignment graph, where max-cliques represent maximal contradiction-free groups of alignments. An…

Desktop app
G T A T C G C T A Estimation by Read… Estimation by Read Depth with Single-nucleotide…

ERDS Estimation by Read Depth with Single-nucleotide variants

An open-source software tool free to academia and nor-profit organization,…

An open-source software tool free to academia and nor-profit organization, designed for inferring copy number variants (CNVs) in high-coverage human genomes using next generation sequence (NGS) data.…

Desktop app
G T A T C G C T A Meerkat Meerkat

Meerkat

To characterize the mutational spectrum of somatic SVs in cancer, it is…

To characterize the mutational spectrum of somatic SVs in cancer, it is important to identify both simple (e.g., deletion, insertion, and inversion) and complex SVs at base-pair resolution. Meerkat…

Desktop app
G T A T C G C T A Generic mUlti-SpliT… Generic mUlti-SpliT Alignment Finder

Gustaf Generic mUlti-SpliT Alignment Finder

A sound generic multi-split SV detection tool that detects and classifies…

A sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of >/=30 bp.

Desktop app
G T A T C G C T A Genome STRucture In… Genome STRucture In Populations

Genome STRiP Genome STRucture In Populations

A suite of tools for discovering and genotyping structural variations using…

A suite of tools for discovering and genotyping structural variations using sequencing data.

Desktop app
G T A T C G C T A LUMPY LUMPY

LUMPY

An extremely flexible probabilistic SV discovery framework that is capable of…

An extremely flexible probabilistic SV discovery framework that is capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence.

Desktop app
G T A T C G C T A TIGRA TIGRA

TIGRA

A computer program that conducts targeted local assembly of structural variants…

A computer program that conducts targeted local assembly of structural variants (SV) using targeted iterative graph routing assembly algorithm. Using data from the 1000 Genomes Project, TIGRA was…

Desktop app
G T A T C G C T A SOAPsv SOAPsv

SOAPsv

A program for detecting the structural variation by whole genome de novo…

A program for detecting the structural variation by whole genome de novo assembly System Requirements.

G T A T C G C T A Cloudbreak Cloudbreak

Cloudbreak

Hadoop-based structural variation (SV) caller for Illumina paired-end DNA…

Hadoop-based structural variation (SV) caller for Illumina paired-end DNA sequencing data.

Desktop app
G T A T C G C T A forestSV forestSV

forestSV

A statistical learning approach, based on Random Forests, that integrates prior…

A statistical learning approach, based on Random Forests, that integrates prior knowledge about the characteristics of structural variants and leads to improved discovery in high-throughput…

Desktop app
G T A T C G C T A Pair Read Informed… Pair Read Informed Split Mapper

PRISM Pair Read Informed Split Mapper

A method that identifies SVs and their precise breakpoints from whole-genome…

A method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling…

Desktop app
G T A T C G C T A Breakway Breakway

Breakway

A suite of programs that take aligned genomic data and report structural…

A suite of programs that take aligned genomic data and report structural variation breakpoints.

Desktop app
G T A T C G C T A SLOPE SLOPE

SLOPE

Detects structural variants from targeted short-DNA reads. Both real and…

Detects structural variants from targeted short-DNA reads. Both real and simulated data are used to demonstrate SLOPE's ability to rapidly detect insertion/deletion events of various sizes as…

Desktop app
G T A T C G C T A micro-read Copy… micro-read Copy Number Variant Regions

mrCaNaVaR micro-read Copy Number Variant Regions

A copy number caller that analyzes the whole-genome next-generation sequence…

A copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. mrCaNaVaR also has the capability of predicting…

Desktop app
G T A T C G C T A IMR-DENOM IMR-DENOM

IMR-DENOM

A package for assembling genomes from Illumina short read sequence data. This…

A package for assembling genomes from Illumina short read sequence data. This package was used to assemble 18 accessions of A. thaliana. IMR/DENOM comprises three independent programs: IMR, DENOM and…

Desktop app
G T A T C G C T A CnD Deprecated CnD

CnD

A program to detect copy number variants from short read sequence data. The…

A program to detect copy number variants from short read sequence data. The target organism is assumed to be inbred, and therefore homozygous, so regions of apparent heterozygous SNPs (as called by…

Advertisements
Join Omic Community

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.