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Inversion detection software tools | Whole-genome sequencing

High-throughput sequencing software tools > Whole-genome sequencing software tools

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.

AGE

OMIC_00305

AGE

An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e.…

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 modification of the alignment scoring scheme(s) that is…

BreakDancer

OMIC_00307

BreakDancer

A Perl/C++ package that provides genome-wide detection of structural variants from next…

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 base pairs to 1 megabase pair that are difficult…

BreaKmer

OMIC_07110

BreaKmer

An approach that uses a 'kmer' strategy to assemble misaligned sequence reads…

An approach that uses a 'kmer' strategy to assemble misaligned sequence reads for predicting insertions, deletions, inversions, tandem duplications and translocations at base-pair resolution in targeted resequencing data. Variants are…

clipcrop

OMIC_00310

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.

Clipping REveals STructure

OMIC_00312

Clipping REveals STructure
CREST

An algorithm using NGS reads with partial alignments to a reference genome to directly…

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 five pediatric T-lineage acute lymphoblastic…

Cortex

OMIC_00056

Cortex

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

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, you can use Cortex to look specifically for…

COSMOS

OMIC_11118

COSMOS

An accurate structural variation (SV) detection method, which compares the statistics of…

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. COSMOS also prioritizes the candidate SVs using…

DELLY

OMIC_00313

DELLY

An integrated structural variant prediction method that can detect deletions, tandem…

An integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.

GASVPro

OMIC_00317

GASVPro

Combines read depth information along with discordant paired-read mappings into a single…

Combines read depth information along with discordant paired-read mappings into a single probabilistic model two common signals of structural variation.

Generic mUlti-SpliT Alignment Finder

OMIC_05195

Generic mUlti-SpliT Alignment Finder
Gustaf

A sound generic multi-split SV detection tool that detects and classifies deletions,…

A sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of >/=30 bp.

inGAP-sv

OMIC_00319

inGAP-sv

Detects and visualizes structural variation from paired-end mapping data. Under this…

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 features, including local depth of coverage, mapping…

LUMPY

OMIC_04674

LUMPY

An extremely flexible probabilistic SV discovery framework that is capable of integrating…

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.

Manta

OMIC_09180

Manta

Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta…

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 large insertions within a single workflow. The…

Meerkat

OMIC_06976

Meerkat

To characterize the mutational spectrum of somatic SVs in cancer, it is important to…

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 predicts both germline and somatic SVs directly…

MetaSV

OMIC_07989

MetaSV

An integrated structural variation (SV) caller which leverages multiple orthogonal SV…

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 SVs. It also analyzes soft-clipped reads from…

Micro-Inversion Detector

OMIC_10997

Micro-Inversion Detector
MID

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

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 different from other variant detection tools is that MID…

Pair Read Informed Split Mapper

OMIC_02288

Pair Read Informed Split Mapper
PRISM

A method that identifies SVs and their precise breakpoints from whole-genome resequencing…

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 breakpoint identification of multiple SV types,…

PBHoney

OMIC_10874

PBHoney

Considers both intra-read discordance and soft-clipped tails of long reads (>10,000…

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 features in a strain of Escherichia coli with…

PEMer

OMIC_00320

PEMer

A computational framework with simulation-based error models for inferring genomic…

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 workflow, SV-Simulation and BreakDB. PEMer workflow is a…

Pindel

OMIC_00321

Pindel

Detects breakpoints of large deletions, medium sized insertions, inversions, tandem…

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 uses a pattern growth approach to identify the…

Sample Heterogeneity Estimation and Assembly by…

OMIC_07018

Sample Heterogeneity Estimation and Assembly by Reference
SHEAR

A tool for next-generation sequencing data analysis that predicts SVs, accounts for…

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 be used for downstream analysis. By utilizing…

SOAPsv

OMIC_04230

SOAPsv

A program for detecting the structural variation by whole genome de novo assembly System…

A program for detecting the structural variation by whole genome de novo assembly System Requirements.

SoftSearch

OMIC_00322

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.

SV-Bay

OMIC_10996

SV-Bay

Detects structural variants in cancer using whole genome sequencing data with or without…

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 assesses changes in the copy number profile and tries…

SVDetect

OMIC_00324

SVDetect

A tool to detect genomic structural variations from paired-end and mate-pair sequencing…

A tool to detect genomic structural variations from paired-end and mate-pair sequencing data.

SVMiner

OMIC_00326

SVMiner

A model-based clustering method for genomic structural variant prediction and genotyping…

A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data.

TakeABreak

OMIC_04836

TakeABreak

A tool that can detect inversion breakpoints directly from raw NGS reads, without the…

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.

VariationHunter

OMIC_00328

VariationHunter

A tool for discovery of structural variation in one or more individuals simultaneously…

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 conflict resolution mechanism that no longer…