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 deletions, deletions with microhomologies and deletions with microsinsertions. The last two types are very common in the human genome, but they pose difficulty for the detection. Furthermore, finding deletions from sequencing data remains challenging. Source text: Zhang et al., 2016.
AGE
AGE
An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e.…
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 modification of the alignment scoring scheme(s) that is…
BreakDancer
BreakDancer
A Perl/C++ package that provides genome-wide detection of structural variants from next…
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 base pairs to 1 megabase pair that are difficult…
BreaKmer
BreaKmer
An approach that uses a 'kmer' strategy to assemble misaligned sequence reads…
An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are…
Breakway
Breakway
A suite of programs that take aligned genomic data and report structural variation…
A suite of programs that take aligned genomic data and report structural variation breakpoints.
CLEVER
CLEVER
An internal segment size based approach, which organizes all, including concordant, reads…
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 algorithm then enumerates all max-cliques and…
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.
Clippers
Clippers
A program designed to identify long deletions of a genome as well as the RNA splicings…
A program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads.
Clipping REveals STructure
Clipping REveals STructure
CREST
An algorithm using NGS reads with partial alignments to a reference genome to directly…
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 five pediatric T-lineage acute lymphoblastic…
Cloudbreak
Cloudbreak
Hadoop-based structural variation (SV) caller for Illumina paired-end DNA sequencing data.
Hadoop-based structural variation (SV) caller for Illumina paired-end DNA sequencing data.
CnD
CnD
A program to detect copy number variants from short read sequence data. The target…
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 MAQ) can be used to detect copy number gains. cnD…
CNV-seq
CNV-seq
A method to detect copy number variation using shotgun sequencing. The method is based on…
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 essential confidence values for detection of CNV.
CNVer
CNVer
A method for CNV detection that supplements the depth-of-coverage with paired-end mapping…
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 variation.
cnvHiTSeq
cnvHiTSeq
A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using…
A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.
CNVnator
CNVnator
An approach to discover, genotype, and characterize typical and atypical CNVs from family…
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 (86%-96%), low false-discovery rate (3%-20%), high…
Control-FREEC
Control-FREEC
A tool for detection of copy-number changes and allelic imbalances (including LOH) using…
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 frequency (BAF) profiles, then calls copy number…
Copy number estimation by a Mixture Of PoissonS
Copy number estimation by a Mixture Of PoissonS
cn.MOPS
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs)…
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 matrices or genomic ranges objects, which are the…
Copy Numbers Of Genes in prokaryotes
Copy Numbers Of Genes in prokaryotes
CNOGpro
Methods for assigning copy number states and breakpoints in resequencing experiments of…
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 methods.
Cortex
Cortex
A tool for genome assembly and variation analysis from sequence data. You can use it to…
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, you can use Cortex to look specifically for…
COSMOS
COSMOS
An accurate structural variation (SV) detection method, which compares the statistics of…
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. COSMOS also prioritizes the candidate SVs using…
DELLY
DELLY
An integrated structural variant prediction method that can detect deletions, tandem…
An integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
Estimation by Read Depth with Single-nucleotide…
Estimation by Read Depth with Single-nucleotide variants
ERDS
An open-source software tool free to academia and nor-profit organization, designed for…
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. When a CNV presents in a test genome, multiple…
FermiKit
FermiKit
A variant calling pipeline for Illumina whole-genome germline data. It de novo assembles…
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 (INDELs) and structural variations (SVs). FermiKit…
forestSV
forestSV
A statistical learning approach, based on Random Forests, that integrates prior knowledge…
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 sequencing data.
GASVPro
GASVPro
Combines read depth information along with discordant paired-read mappings into a single…
Combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation.
Generic mUlti-SpliT Alignment Finder
Generic mUlti-SpliT Alignment Finder
Gustaf
A sound generic multi-split SV detection tool that detects and classifies deletions,…
A sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of >/=30 bp.
Genome STRucture In Populations
Genome STRucture In Populations
Genome STRiP
A suite of tools for discovering and genotyping structural variations using sequencing…
A suite of tools for discovering and genotyping structural variations using sequencing data.
Geometric Analysis of Structural Variants
Geometric Analysis of Structural Variants
GASV
A tool for identifying structural variants (SVs) from paired-end sequencing data. GASV is…
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 represents the uncertainty in measurement of a…
IMR-DENOM
IMR-DENOM
A package for assembling genomes from Illumina short read sequence data. This package was…
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 MCMERGE.
inGAP-sv
inGAP-sv
Detects and visualizes structural variation from paired-end mapping data. Under this…
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 features, including local depth of coverage, mapping…
JointSLM
JointSLM
An algorithm that extend the univariate SLM to the multivariate case in order to detect…
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 the signal to noise ratio (SNR) of the data:…
LUMPY
LUMPY
An extremely flexible probabilistic SV discovery framework that is capable of integrating…
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.
Manta
Manta
Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta…
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 large insertions within a single workflow. The…
Meerkat
Meerkat
To characterize the mutational spectrum of somatic SVs in cancer, it is important to…
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 predicts both germline and somatic SVs directly…
Mendelian-inheritance-AtTEntive…
Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder
MATE-CLEVER
An approach that accurately discovers and genotypes indels longer than 30 bp from…
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 quartets, MATE-CLEVER integrates statistics that…
MetaSV
MetaSV
An integrated structural variation (SV) caller which leverages multiple orthogonal SV…
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 SVs. It also analyzes soft-clipped reads from…
micro-read Copy Number Variant Regions
micro-read Copy Number Variant Regions
mrCaNaVaR
A copy number caller that analyzes the whole-genome next-generation sequence mapping read…
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 absolute copy numbers of genomic intervals.
Pair Read Informed Split Mapper
Pair Read Informed Split Mapper
PRISM
A method that identifies SVs and their precise breakpoints from whole-genome resequencing…
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 breakpoint identification of multiple SV types,…
PBHoney
PBHoney
Considers both intra-read discordance and soft-clipped tails of long reads (>10,000…
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 features in a strain of Escherichia coli with…
PEMer
PEMer
A computational framework with simulation-based error models for inferring genomic…
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 workflow, SV-Simulation and BreakDB. PEMer workflow is a…
Pindel
Pindel
Detects breakpoints of large deletions, medium sized insertions, inversions, tandem…
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 uses a pattern growth approach to identify the…
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 specificity. Platypus can detect SNPs, MNPs, short…
RDXplorer
RDXplorer
A computational tool for copy number variants (CNV) detection in whole human genome…
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 read depth coverage is estimated in…
ReAd Pair spliT Read-Structural Variant
ReAd Pair spliT Read-Structural Variant
RAPTR-SV
A program designed to process previously aligned, Illumina Paired-end whole genome…
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 using RAPTR-SV and other, similar algorithms for SV…
readDepth
readDepth
This package for R can detect copy number aberrations by measuring the depth of coverage…
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 does not require the sequencing of a reference…
Repeat
Repeat
Allows the repeat-aware and error-tolerant comparison of deletion predictions given in…
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, such as 50% reciprocal overlap substantially.
Sample Heterogeneity Estimation and Assembly by…
Sample Heterogeneity Estimation and Assembly by Reference
SHEAR
A tool for next-generation sequencing data analysis that predicts SVs, accounts for…
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 be used for downstream analysis. By utilizing…
SLOPE
SLOPE
Detects structural variants from targeted short-DNA reads. Both real and simulated data…
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 well as translocations and viral integration sites…
SOAPsv
SOAPsv
A program for detecting the structural variation by whole genome de novo assembly System…
A program for detecting the structural variation by whole genome de novo assembly System Requirements.
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.
Sprites
Sprites
Finds deletions from sequencing data. Sprites aligns a whole soft-clipping read rather…
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, in order to find the longest prefix or suffix of…
SV-Bay
SV-Bay
Detects structural variants in cancer using whole genome sequencing data with or without…
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 assesses changes in the copy number profile and tries…
SVClassify
SVClassify
Calculates annotations from one or more aligned bam files from many high-throughput…
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 variants (SVs) as likely true or false positives.…
SVDetect
SVDetect
A tool to detect genomic structural variations from paired-end and mate-pair sequencing…
A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.
SVMiner
SVMiner
A model-based clustering method for genomic structural variant prediction and genotyping…
A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data.
SVseq
SVseq
An improved approach for accurate and efficient calling of structural variations with…
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
TIGRA
TIGRA
A computer program that conducts targeted local assembly of structural variants (SV)…
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 able to accurately assemble the majority of deletion…
TrioCNV
TrioCNV
A tool designed to jointly detecting copy number variations (CNVs) from whole genome…
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 to accommodate over-dispersion and considered GC…
VarDict
VarDict
A versatile variant caller for both DNA- and RNA-sequencing data. VarDict contains many…
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 realignment, built-in capability of de-duplication,…
VariationHunter
VariationHunter
A tool for discovery of structural variation in one or more individuals simultaneously…
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 conflict resolution mechanism that no longer…
ViVar
ViVar
A comprehensive analysis platform for the processing, analysis and visualization of…
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 loci or genes. Vivar allows you to scale your…