Inversion. A segment of DNA that is reversed in orientation with respect to the rest of the chromosome. Pericentric inversions include the centromere, whereas paracentric inversions do not. Source text: Feuk et al., 2006.

Desktop app
G T A T C G C T A BreakDancer BreakDancer

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…

Desktop app
G T A T C G C T A Cortex Cortex

Cortex

A tool for genome assembly and variation analysis from sequence data. You can…

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,…

Web app
G T A T C G C T A Clipping REveals… Clipping REveals STructure

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…

Desktop app
G T A T C G C T A Pindel Pindel

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…

Desktop app
G T A T C G C T A PEMer PEMer

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…

Desktop app
G T A T C G C T A DELLY DELLY

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…

Desktop app
G T A T C G C T A GASVPro GASVPro

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.

Desktop app
G T A T C G C T A VariationHunter VariationHunter

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…

Desktop app
G T A T C G C T A SVDetect SVDetect

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.

Desktop app
G T A T C G C T A inGAP-sv inGAP-sv

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…

Desktop app
G T A T C G C T A AGE AGE

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…

Desktop app
G T A T C G C T A SoftSearch 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.

Desktop app
G T A T C G C T A clipcrop 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.

Desktop app
G T A T C G C T A SVMiner SVMiner

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.

Desktop app
G T A T C G C T A PSSV PSSV

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,…

Desktop app
G T A T C G C T A VarDict VarDict

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…

Desktop app
G T A T C G C T A Manta Manta

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…

Desktop app
G T A T C G C T A BreaKmer BreaKmer

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…

Desktop app
G T A T C G C T A Structural Variation… Structural Variation detection by STAck and Tail

SV-STAT Structural Variation detection by STAck and Tail

A statistical tool to quantify evidence for structural variation in genomic…

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

Desktop app
G T A T C G C T A Maximal Unique… Maximal Unique Matchdex

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…

Desktop app
G T A T C G C T A SRinversion SRinversion

SRinversion

A framework to analyze poorly mapped or unmapped reads by splitting and…

A framework to analyze poorly mapped or unmapped reads by splitting and re-aligning them for the purpose of inversion detection. SRinversion consists of 4 steps: 1) extract poorly mapped reads, 2)…

Desktop app
G T A T C G C T A Duplication and… Duplication and Inversion GenoTYPER

DIGTYPER Duplication and Inversion GenoTYPER

A method to genotype tandem duplications and inversions. DIGTYPER computes…

A method to genotype tandem duplications and inversions. DIGTYPER computes genotype likelihoods for a given inversion or duplication and reports the maximum likelihood genotype. In contrast to purely…

Desktop app
G T A T C G C T A COSMOS COSMOS

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.…

Desktop app
G T A T C G C T A Micro-Inversion… Micro-Inversion Detector

MID Micro-Inversion Detector

Identifies micro-inversions (MIs) in human genomes using next-generation…

Identifies micro-inversions (MIs) in human genomes using next-generation sequencing reads. The algorithm of MID is designed based on a dynamic programming path-finding approach. What makes MID…

Desktop app
G T A T C G C T A SV-Bay SV-Bay

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…

Desktop app
G T A T C G C T A PBHoney PBHoney

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…

Desktop app
G T A T C G C T A MetaSV MetaSV

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…

Desktop app
G T A T C G C T A Sample Heterogeneity… Sample Heterogeneity Estimation and Assembly by…

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…

Desktop app
G T A T C G C T A Meerkat Meerkat

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…

Desktop app
G T A T C G C T A Generic mUlti-SpliT… Generic mUlti-SpliT Alignment Finder

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.

Desktop app
G T A T C G C T A TakeABreak TakeABreak

TakeABreak

A tool that can detect inversion breakpoints directly from raw NGS reads,…

A tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes.

Desktop app
G T A T C G C T A LUMPY LUMPY

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.

Desktop app
G T A T C G C T A SOAPsv SOAPsv

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.

Desktop app
G T A T C G C T A Pair Read Informed… Pair Read Informed Split Mapper

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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