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Insertion detection software tools | Whole-genome sequencing data analysis

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IMR-DENOM
Desktop

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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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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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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Platypus
Desktop

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…

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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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MATE-CLEVER
Desktop

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…

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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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SWAN
Desktop

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…

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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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Breakway
Desktop

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.

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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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HySA
Desktop

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…

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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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NovelSeq
Desktop

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.

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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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Seeksv
Desktop

Seeksv

Detects somatic structural variations (SVs) and viral integration events.…

Detects somatic structural variations (SVs) and viral integration events. Seeksv simultaneously uses split read signal, discordant paired-end read signal, read depth signal and the fragment with two…

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RAPTR-SV
Desktop

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…

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SLOPE
Desktop

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…

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SVseq
Desktop

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.

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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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Reprever
Desktop

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…

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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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PopIns
Desktop

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…

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SVClassify
Desktop

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…

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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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ANISE and BASIL
Desktop

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…

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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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MindTheGap
Desktop

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…

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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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ViVar
Web

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…

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Cassiopee-c
Desktop

Cassiopee-c

Searches a subsequence from a genomic sequence. Cassiopee-c is able to find…

Searches a subsequence from a genomic sequence. Cassiopee-c is able to find exact match and allows substitutions, insertions and deletions. It can make indexation based on a suffix tree with…

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Cloudbreak
Desktop

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.

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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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