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Inversion detection software tools | Whole-genome sequencing data analysis

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)Structural variation in the…
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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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SMRT-SV
Desktop

SMRT-SV

Allows to identify missing sequence and genetic variation. SMRT-SV generates…

Allows to identify missing sequence and genetic variation. SMRT-SV generates data about DNA sequences. The distinctive feature of this tool is that native DNA is sequenced without cloning or…

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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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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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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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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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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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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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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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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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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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VALOR
Desktop

VALOR variation using long range information

Allows to search both read pair and split clone sequence signatures using the…

Allows to search both read pair and split clone sequence signatures using the mapping locations of long range sequencing read. VALOR requires split clones from different pools to cluster at the same…

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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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SRinversion
Desktop

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)…

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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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MID
Desktop

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…

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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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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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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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DIGTYPER
Desktop

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…

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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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TakeABreak
Desktop

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.

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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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