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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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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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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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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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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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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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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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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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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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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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