Desktop app
G T A T C G C T A Platypus Platypus

Platypus

A tool designed for efficient and accurate variant-detection in high-throughput…

A tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high…

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 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 Mendelian-inheritance-AtTEntive…

MATE-CLEVER Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder

An approach that accurately discovers and genotypes indels longer than 30 bp…

An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios 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 SVseq SVseq

SVseq

An improved approach for accurate and efficient calling of structural…

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence 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 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 Statistical… Statistical Structural Variant Analysis for NGS

SWAN Statistical Structural Variant Analysis for NGS

A statistical framework and algorithm for structural variant (SV) detection…

A statistical framework and algorithm for structural variant (SV) detection from whole genome sequencing data. SWAN integrates multiple features, including insert size, hanging read pairs and read…

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 Seeksv Seeksv

Seeksv

An accurate tool for detecting somatic structural variations (SVs) and viral…

An accurate tool for detecting somatic structural variations (SVs) and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and…

Desktop app
G T A T C G C T A Hybrid Structural… Hybrid Structural variant Assembly

HySA Hybrid Structural variant Assembly

Integrates sequencing reads from next-generation sequencing (NGS) and…

Integrates sequencing reads from next-generation sequencing (NGS) and single-molecule sequencing (SMS) technologies to accurately assemble and detect structural variations (SV) in human genome. By…

Desktop app
G T A T C G C T A SVClassify SVClassify

SVClassify

Calculates annotations from one or more aligned bam files from many…

Calculates annotations from one or more aligned bam files from many high-throughput sequencing technologies, and then builds a one-class model using these annotations to classify candidate structural…

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 PopIns PopIns

PopIns

A method for discovering and genotyping novel sequence insertions. PopIns takes…

A method for discovering and genotyping novel sequence insertions. PopIns takes as input a reads-to-reference alignment, assembles unaligned reads using a standard assembly tool, merges the contigs…

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 ANISE and BASIL ANISE and BASIL

ANISE and BASIL

Tools for insert site detection and for the assembly of novel insertions. BASIL…

Tools for insert site detection and for the assembly of novel insertions. BASIL features an efficient sliding window implementation for clustering read alignments at insertion sites and clipping…

Desktop app
G T A T C G C T A ReAd Pair spliT… ReAd Pair spliT Read-Structural Variant

RAPTR-SV ReAd Pair spliT Read-Structural Variant

A program designed to process previously aligned, Illumina Paired-end whole…

A program designed to process previously aligned, Illumina Paired-end whole genome sequence data to identify structural variants such as deletions, insertions and tandem duplications. Simulations…

Web app
G T A T C G C T A ViVar ViVar

ViVar

A comprehensive analysis platform for the processing, analysis and…

A comprehensive analysis platform for the processing, analysis and visualization of structural variation based on sequencing data or genomic microarrays, enabling the rapid identification of disease…

Desktop app
G T A T C G C T A CLEVER CLEVER

CLEVER

An internal segment size based approach, which organizes all, including…

An internal segment size based approach, which organizes all, including concordant, reads into a read alignment graph, where max-cliques represent maximal contradiction-free groups of alignments. An…

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 MindTheGap MindTheGap

MindTheGap

A software tool that performs detection and assembly of DNA insertion variants…

A software tool that performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome. MindTheGap is designed to call insertions of any size, whether…

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 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.

G T A T C G C T A Cloudbreak Cloudbreak

Cloudbreak

Hadoop-based structural variation (SV) caller for Illumina paired-end DNA…

Hadoop-based structural variation (SV) caller for Illumina paired-end DNA sequencing data.

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…

Desktop app
G T A T C G C T A Breakway Breakway

Breakway

A suite of programs that take aligned genomic data and report structural…

A suite of programs that take aligned genomic data and report structural variation breakpoints.

Desktop app
G T A T C G C T A NovelSeq NovelSeq

NovelSeq

It is designed to detect novel sequence insertions using high throughput…

It is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

Desktop app
G T A T C G C T A SLOPE SLOPE

SLOPE

Detects structural variants from targeted short-DNA reads. Both real and…

Detects structural variants from targeted short-DNA reads. Both real and simulated data are used to demonstrate SLOPE's ability to rapidly detect insertion/deletion events of various sizes as…

Desktop app
G T A T C G C T A Reprever Reprever

Reprever

Given paired-end mapped reads and a candidate high-copy region, Reprever…

Given paired-end mapped reads and a candidate high-copy region, Reprever identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence…

Desktop app
G T A T C G C T A IMR-DENOM IMR-DENOM

IMR-DENOM

A package for assembling genomes from Illumina short read sequence data. This…

A package for assembling genomes from Illumina short read sequence data. This package was used to assemble 18 accessions of A. thaliana. IMR/DENOM comprises three independent programs: IMR, DENOM and…

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