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Deletion detection software tools | Whole-genome sequencing

High-throughput sequencing software tools > Whole-genome sequencing software tools

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

OMIC_00305

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

OMIC_00307

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

OMIC_07110

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

OMIC_02176

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

OMIC_06977

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

OMIC_00310

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

OMIC_00311

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

OMIC_00312

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

OMIC_04078

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

OMIC_00338

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

OMIC_00339

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

OMIC_00341

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

OMIC_00342

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

OMIC_00343

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

OMIC_00344

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

OMIC_00335

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

OMIC_07466

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

OMIC_00056

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

OMIC_11118

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

OMIC_00313

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…

OMIC_06978

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

OMIC_09503

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

OMIC_03839

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

OMIC_00317

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

OMIC_05195

Generic mUlti-SpliT Alignment Finder
Gustaf

Genome STRucture In Populations

OMIC_05101

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

OMIC_01352

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

OMIC_06975

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

OMIC_00319

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

OMIC_00346

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

OMIC_04674

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

OMIC_09180

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

OMIC_06976

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…

OMIC_00309

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

MetaSV

OMIC_07989

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

OMIC_02138

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

OMIC_02288

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

OMIC_10874

PBHoney

PEMer

OMIC_00320

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

OMIC_00321

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

OMIC_00068

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

OMIC_00349

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

OMIC_07570

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

OMIC_00350

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

OMIC_08667

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…

OMIC_07018

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

OMIC_02169

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

OMIC_04230

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

OMIC_00322

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

OMIC_11119

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

OMIC_10996

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

OMIC_11029

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

OMIC_00324

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

OMIC_00326

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

OMIC_00327

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

OMIC_04667

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

OMIC_11017

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

OMIC_11609

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

OMIC_00328

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

OMIC_07111

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…