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Structural variant detection software tools | Whole-genome sequencing

From prokaryotes to eukaryotes, phenotypic variation, adaptation and speciation has been associated with structural variation between genomes of individuals within the same species. Many computer algorithms detecting such variations (callers) have…
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BreakSeq
Desktop

BreakSeq

Database of known human breakpoint junctions and software to search short reads…

Database of known human breakpoint junctions and software to search short reads against them.

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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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novoBreak
Desktop

novoBreak

A tool to generate local assemblies of breakpoints genome-wide. NovoBreak is an…

A tool to generate local assemblies of breakpoints genome-wide. NovoBreak is an algorithm used in cancer genomic studies to discover structural variants (both somatic and germline) breakpoints in…

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Hydra-sv
Desktop

Hydra-sv

Detects structural variation (SV) breakpoints by clustering discordant…

Detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose "signatures" corroborate the same putative breakpoint.

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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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GRIMM
Web
Desktop

GRIMM Genome Rearrangements in Man and Mouse

Combines pairwise distance and rearrangement algorithms for unichromosomal and…

Combines pairwise distance and rearrangement algorithms for unichromosomal and multichromosomal genomes. GRIMM can be run with signed or unsigned gene data. The application calculates the lowest…

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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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nFuse
Desktop

nFuse

Predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole…

Predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

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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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APOLLOH
Desktop

APOLLOH

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and…

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

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SVMerge
Desktop

SVMerge

A pipeline to detect structural variants (SVs) by integrating calls from…

A pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly.

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ReMixT
Desktop

ReMixT

Tries to improve both inference and interpretation of copy number changes and…

Tries to improve both inference and interpretation of copy number changes and genomic rearrangements. ReMixT work about prediction of clone fraction, clone specific copy number, and clone specificity…

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SVelter
Desktop

SVelter

Identifies regions of the genome suspected to harbor a complex event. SVelter…

Identifies regions of the genome suspected to harbor a complex event. SVelter then resolves the structure by iteratively rearranging the local genome structure, in a randomized fashion, with each…

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FusionMap
Desktop

FusionMap

An efficient fusion aligner which aligns reads spanning fusion junctions…

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions.

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VariantTools
Desktop

VariantTools

Decides whether a variant is callable, based on coverage and a power…

Decides whether a variant is callable, based on coverage and a power calculation. VariantTools was tested by loading some precomputed nucleotide tallies. It permits to explore different filtering…

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GenomeVIP
Desktop

GenomeVIP Genome Variant Investigation Platform

Performs variant discovery on Amazon's Web Service (AWS) cloud or on local…

Performs variant discovery on Amazon's Web Service (AWS) cloud or on local high-performance computing clusters. GenomeVIP is a genomics analysis pipeline for cloud computing with germline and…

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Socrates
Desktop

Socrates

A method for detecting genomic rearrangements in tumours that utilises only…

A method for detecting genomic rearrangements in tumours that utilises only split-read data.

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deStruct
Desktop

deStruct

Allows joint prediction of rearrangement breakpoints from single or multiple…

Allows joint prediction of rearrangement breakpoints from single or multiple tumor samples. deStruct is a software which identifies breakpoints, and assigns read alignments to those breakpoints. The…

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PeSV-Fisher
Desktop

PeSV-Fisher

Detects and characterizes structural variants (SVs) using next-generation…

Detects and characterizes structural variants (SVs) using next-generation sequencing (NGS) data. PeSV-Fisher is based on a combinatorial analysis of paired-reads (PR) and read-depth (RD) strategies…

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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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Wham
Desktop

Wham WHole-genome Alignment Metrics

A structural variant (SV) caller that integrates several sources of mapping…

A structural variant (SV) caller that integrates several sources of mapping information to identify SVs. Wham classifies SVs using a flexible and extendable machine-learning algorithm (random…

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Tardis
Desktop

Tardis

Permits to automate and discover structural variations (SVs). Tardis is a…

Permits to automate and discover structural variations (SVs). Tardis is a toolkit that integrates read pair, read depth, and split read (using soft clipped mappings) sequence signatures to discover…

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PECaller
Desktop

PECaller

Allows to minimize the burden on networks and disk arrays. PECaller allows the…

Allows to minimize the burden on networks and disk arrays. PECaller allows the imposition of a population genetics-inspired prior on the data and the ability to fit sophisticated models of read…

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GORpipe
Desktop

GORpipe

Works with large volumes of DNA sequence data. GORpipe can be used to annotate…

Works with large volumes of DNA sequence data. GORpipe can be used to annotate sequence variants, find genomic spatial overlap between various types of genomic features, filter and aggregate them in…

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ASDPex
Desktop

ASDPex

Analyzes individual Variant calling format (VCF) files with the goal of…

Analyzes individual Variant calling format (VCF) files with the goal of identifying alignable scaffold-discrepant position (ASDP)-associated variants. ASDPex is an implementation an ASDP extraction…

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CLOVE
Desktop

CLOVE

Integrates calls from one or more breakpoint detection methods and classifies…

Integrates calls from one or more breakpoint detection methods and classifies the structural variant (SV). CLOVE can build a graph data structure from the provided breakpoint information and then…

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Breakpointer
Desktop

Breakpointer

A fast tool for locating sequence breakpoints from the alignment of single end…

A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS).

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SVachra
Desktop

SVachra Structural Variation Assesment of CHRomosomal Aberrations

Detects chromosomal aberrations with high specificity across a several variant…

Detects chromosomal aberrations with high specificity across a several variant types and lengths in next-generation mate pair sequencing data. SVachra calculates the distributions of the inward and…

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MrMosaic
Desktop

MrMosaic

Allows users to detect structural mosaicism abnormalities in targeted or…

Allows users to detect structural mosaicism abnormalities in targeted or whole-genome sequencing (WGS) data. MrMosaic measures deviations in copy number and allele frequency by comparison between…

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GVC
Desktop

GVC Genomic Variant Caller

Detects various genomic variants including single nucleotide variant (SNV),…

Detects various genomic variants including single nucleotide variant (SNV), single insertion/deletion (sINDEL) and structural variation (SV) from personal and normal-cancer paired whole-genome/exome…

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rMFilter
Desktop

rMFilter region Match-based Filter

Identifies chimeric noisy long reads based on short token matches within local…

Identifies chimeric noisy long reads based on short token matches within local genomic regions. rMFilter can accelerate structure variation (SV) calling pipelines without loss of effectiveness. It is…

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Pysim-sv
Desktop

Pysim-sv

Simulates structural variation. Pysim-sv is a package for simulating…

Simulates structural variation. Pysim-sv is a package for simulating high-throughput sequencing (HTS) data to evaluate performance of structural variation (SV) detection algorithms. Pysim-sv can…

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SV2
Desktop

SV2 support-vector structural-variant genotyper

Implements a machine-learning algorithm for genotyping deletions and tandem…

Implements a machine-learning algorithm for genotyping deletions and tandem duplications from paired-end whole genome sequencing (WGS) data. SV2 can rapidly integrate variant calls from multiple…

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SvABA
Desktop

SvABA Structural variation and indel Analysis By Assembly

Detects structural variants (SVs) from short-read sequencing data using…

Detects structural variants (SVs) from short-read sequencing data using genome-wide local assembly with low memory and computing requirements. SvABA’s performance was evaluated on the NA12878 human…

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VaPoR
Desktop

VaPoR

Validates large structural variant (SV) sets using long read sequencing data.…

Validates large structural variant (SV) sets using long read sequencing data. VaPoR provides a highly efficient algorithm that scores each SV prediction by autonomously analyzing the recurrence of…

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GRIDSS
Desktop

GRIDSS Genomic Rearrangement IDentification Software Suite

Allows identification of genomic rearrangements. GRIDSS is a module software…

Allows identification of genomic rearrangements. GRIDSS is a module software suite containing tools which performs genome-wide break-end assembly prior to variant calling using a positional de Bruijn…

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Hydra-Multi
Desktop

Hydra-Multi

A paired-end read structural variant discovery tool that is capable of…

A paired-end read structural variant discovery tool that is capable of integrating signals from hundreds of samples. Given the increasing number of large-scale genome sequencing projects, the rapid…

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Ulysses
Desktop

Ulysses

A tool that achieves drastically higher detection accuracy than existing tools,…

A tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high…

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iSVP
Desktop

iSVP integrated Structural Variant calling Pipeline

Allows detection of structural variants (SV) from next-generation sequencing…

Allows detection of structural variants (SV) from next-generation sequencing (NGS) data. iSVP is a pipeline that combines existing SV detection methods. The software was applied to human whole genome…

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BreakTrans
Desktop

BreakTrans

A computer program that maps predicted gene fusions to genomic structural…

A computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events and provide them mechanism/functional interpretation.

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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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targetSeqView
Desktop

targetSeqView

A probability-based score and visualization method to aid in distinguishing…

A probability-based score and visualization method to aid in distinguishing true structural variants from alignment artifacts. targetSeqView is able to separate real structural variants from false…

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MultiBreak-SV
Desktop

MultiBreak-SV

Recent "third-generation" sequencing technologies provide…

Recent "third-generation" sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. MultiBreak-SV…

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hot_scan
Desktop

hot_scan

A free software to detect genomic regions unusually rich in translocation…

A free software to detect genomic regions unusually rich in translocation breakpoints.

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SlideSort-BPR
Desktop

SlideSort-BPR

A reference-free method for detecting clusters of breakpoints from the…

A reference-free method for detecting clusters of breakpoints from the chromosomal rearrangements.

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RawGeno
Desktop

RawGeno

Proceeds to the binning and scoring of amplified fragmen-length polymorphisms…

Proceeds to the binning and scoring of amplified fragmen-length polymorphisms (AFLP) electropherograms. RawGeno includes several filters to assess the quality of electropherograms and checks the…

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PREGO
Desktop

PREGO Paired-end Reconstruction of Genome Organization

An algorithm that reconstructs a cancer genome as a rearrangement of segments,…

An algorithm that reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired-end sequencing data. PREGO identifies complex and biologically…

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DangerTrack
Desktop

DangerTrack

Evaluates difficult to assess regions that uses Structural variation (SV) calls…

Evaluates difficult to assess regions that uses Structural variation (SV) calls and map ability to generate a genome-wide score. DangerTrack is a package that contents: (i) generated DangerTrack…

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SVCompare
Desktop

SVCompare

Compares and estimates breakpoints for Structural variation (SV) across…

Compares and estimates breakpoints for Structural variation (SV) across different technologies and resources. SVCompare is a collection of methods developed to analyze, annotate and more accurately…

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SquareDancer
Desktop

SquareDancer

This tool identifies SVs or splice junctions from soft-clipped genomic or cDNA…

This tool identifies SVs or splice junctions from soft-clipped genomic or cDNA reads.

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