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Deletion detection software tools | Whole-genome sequencing data analysis

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…
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IMR-DENOM
Desktop

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…

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CNVnator
Desktop

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…

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Cortex
Desktop

Cortex

Allows de novo genome assembly and multisample variant calling. Cortex is a…

Allows de novo genome assembly and multisample variant calling. Cortex is a modular set of multi-threaded programs for manipulating assembly graphs. Linked de Bruijn Graph (LdBG) data structure and…

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SV-STAT
Desktop

SV-STAT Structural Variation detection by STAck and Tail

Quantifies evidence for structural variation in genomic regions suspected of…

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

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FRT Deletion…
Web

FRT Deletion Hunter

Provides systematic isolation of targeted deletions in the D. melanogaster…

Provides systematic isolation of targeted deletions in the D. melanogaster genome. FRT Deletion Hunter can be useful to improve the Stock Center deletion collection. It is able to generate small…

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Platypus
Desktop

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…

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mrCaNaVaR
Desktop

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…

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BreakDancer
Desktop

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…

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SOAPsv
Desktop

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.

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CREST
Web

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…

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forestSV
Desktop

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…

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Control-FREEC
Desktop

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…

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Genome STRiP
Desktop

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.

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Pindel
Desktop

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…

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cn.MOPS
Desktop

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…

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Meerkat
Desktop

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…

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DELLY
Desktop

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…

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RDXplorer
Desktop

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…

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MATE-CLEVER
Desktop

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…

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cnvHiTSeq
Desktop

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.

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PEMer
Desktop

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…

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GASV
Desktop

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…

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CNVer
Desktop

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…

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SWAN
Desktop

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…

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VarDict
Desktop

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…

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Clippers
Desktop

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.

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GASVPro
Desktop

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.

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PSSV
Desktop

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,…

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inGAP-sv
Desktop

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…

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Breakway
Desktop

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.

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JointSLM
Desktop

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…

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VariationHunter
Desktop

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…

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SVDetect
Desktop

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.

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CNV-seq
Desktop

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…

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COSMOS
Desktop

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.…

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PRISM
Desktop

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…

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Sniffles
Desktop

Sniffles

Provides a structural variation (SV) caller for long reads. Sniffles is mainly…

Provides a structural variation (SV) caller for long reads. Sniffles is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions,…

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AGE
Desktop

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…

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RAPTR-SV
Desktop

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…

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CNOGpro
Desktop

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…

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CnD
Desktop

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…

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SLOPE
Desktop

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…

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readDepth
Desktop

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…

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SVseq
Desktop

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.

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BreaKmer
Desktop

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…

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Sprites
Desktop

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,…

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TrioCNV
Desktop

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…

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SV-Bay
Desktop

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…

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Manta
Desktop

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…

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TIGRA
Desktop

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…

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SVClassify
Desktop

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…

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SoftSearch
Desktop

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.

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DeF-GPU
Desktop

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…

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clipcrop
Desktop

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.

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FermiKit
Desktop

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…

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Repeat
Desktop

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,…

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MetaSV
Desktop

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…

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PBHoney
Desktop

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…

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LUMPY
Desktop

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.

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SVMiner
Desktop

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.

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SV-AUTOPILOT
Desktop

SV-AUTOPILOT Structural Variation AUTOmated PIpeLine Optimization Tool

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is…

Standardizes the Structural Variation (SV) detection pipeline. SV-AUTOPILOT is a pipeline that can be used on existing computing infrastructure in the form of a Virtual Machine (VM) Image. It…

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MUMdex
Desktop

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…

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Gustaf
Desktop

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.

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SHEAR
Desktop

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…

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ViVar
Web

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…

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Cassiopee-c
Desktop

Cassiopee-c

Searches a subsequence from a genomic sequence. Cassiopee-c is able to find…

Searches a subsequence from a genomic sequence. Cassiopee-c is able to find exact match and allows substitutions, insertions and deletions. It can make indexation based on a suffix tree with…

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Cloudbreak
Desktop

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.

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SVmine
Desktop

SVmine

Employs a two-stage process to evaluate and refine structural variation (SV)…

Employs a two-stage process to evaluate and refine structural variation (SV) predictions. SVmine is an algorithm for further mining of SV predictions from multiple algorithms to improve the…

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ERDS
Desktop

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.…

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