Segmental duplication or low-copy repeat. A segment of DNA >1 kb in size that occurs in two or more copies per haploid genome, with the different copies sharing >90% sequence identity. They are often variable in copy number and can therefore also be CNVs.Source text:(Feuk…
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CNVnator
Desktop

CNVnator

An approach to discover, genotype, and characterize typical and atypical CNVs…

An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Overall, for CNVs accessible by RD, CNVnator has high sensitivity…

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Control-FREEC
Desktop

Control-FREEC

A tool for detection of copy-number changes and allelic imbalances (including…

A tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. Control-FREEC automatically computes, normalizes, segments copy number and beta allele…

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RDXplorer
Desktop

RDXplorer

A computational tool for copy number variants (CNV) detection in whole human…

A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm. The…

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CNVer
Desktop

CNVer

A method for CNV detection that supplements the depth-of-coverage with…

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of…

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cn.MOPS
Desktop

cn.MOPS Copy number estimation by a Mixture Of PoissonS

A data processing pipeline for copy number variations and aberrations (CNVs and…

A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count…

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JointSLM
Desktop

JointSLM

An algorithm that extend the univariate SLM to the multivariate case in order…

An algorithm that extend the univariate SLM to the multivariate case in order to detect recurrent shifts in the mean of multiple sequential processes. The resolution of JointSLM strictly depends on…

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cnvHiTSeq
Desktop

cnvHiTSeq

A set of Java-based command-line tools for detecting Copy Number Variants…

A set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data.

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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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GASV
Desktop

GASV Geometric Analysis of Structural Variants

A tool for identifying structural variants (SVs) from paired-end sequencing…

A tool for identifying structural variants (SVs) from paired-end sequencing data. GASV is a geometric approach for identification, classification and comparison of structural variants. This approach…

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CNV-seq
Desktop

CNV-seq

A method to detect copy number variation using shotgun sequencing. The method…

A method to detect copy number variation using shotgun sequencing. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of…

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readDepth
Desktop

readDepth

This package for R can detect copy number aberrations by measuring the depth of…

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In contrast to other published methods, readDepth…

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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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CTDGFinder
Desktop

CTDGFinder

Formalizes and automates the identification of clusters of tandemly duplicated…

Formalizes and automates the identification of clusters of tandemly duplicated genes (CTDGs) by examining the physical distribution of individual members of families of duplicated genes across…

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GECKO-CSB
Desktop

GECKO-CSB GEnome Comparison with K-mers Out-of-core-Computational Synteny Block

A package which detects and identifies blocks of large rearrangements taking…

A package which detects and identifies blocks of large rearrangements taking into account repeats, tandem repeats and duplications, starting with the simple collection of ungapped local alignments.…

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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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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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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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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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TrioCNV
Desktop

TrioCNV

A tool designed to jointly detecting copy number variations (CNVs) from whole…

A tool designed to jointly detecting copy number variations (CNVs) from whole genome sequencing data in parent-offspring trios. TrioCNV models read depth signal with the negative binomial regression…

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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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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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CNOGpro
Desktop

CNOGpro Copy Numbers Of Genes in prokaryotes

Methods for assigning copy number states and breakpoints in resequencing…

Methods for assigning copy number states and breakpoints in resequencing experiments of prokaryotic organisms. CNOGpro will in some cases represent a significant jump in accuracy from other current…

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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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ERDS
Desktop

ERDS Estimation by Read Depth with Single-nucleotide variants

An open-source software tool free to academia and nor-profit organization,…

An open-source software tool free to academia and nor-profit organization, designed for inferring copy number variants (CNVs) in high-coverage human genomes using next generation sequence (NGS) data.…

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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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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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forestSV
Desktop

forestSV

A statistical learning approach, based on Random Forests, that integrates prior…

A statistical learning approach, based on Random Forests, that integrates prior knowledge about the characteristics of structural variants and leads to improved discovery in high-throughput…

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mrCaNaVaR
Desktop

mrCaNaVaR micro-read Copy Number Variant Regions

A copy number caller that analyzes the whole-genome next-generation sequence…

A copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. mrCaNaVaR also has the capability of predicting…

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CnD
Desktop

CnD

A program to detect copy number variants from short read sequence data. The…

A program to detect copy number variants from short read sequence data. The target organism is assumed to be inbred, and therefore homozygous, so regions of apparent heterozygous SNPs (as called by…

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