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Copy number variation detection software tools | Whole-genome sequencing data analysis

Copy number variation (CNV) is a common source of genetic variation that has been implicated in many genomic disorders. CNV is a form of structural variation (SV) in the genome. Usually, CNV refers to the duplication or deletion of DNA segments…
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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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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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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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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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SegSeq
Desktop

SegSeq

A computational algorithm to detect and localize copy-number alterations from…

A computational algorithm to detect and localize copy-number alterations from massively parallel sequence data. SegSeq is a hybrid of local change-point analysis with a subsequent merging procedure…

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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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BIC-seq
Desktop

BIC-seq

Combines normalization of the data at the nucleotide level and Bayesian…

Combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline copy number variations (CNVs) accurately. Whereas…

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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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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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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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WISECONDOR
Desktop

WISECONDOR WIthin-SamplE COpy Number aberration DetectOR

A set of python scripts that detects fetal chromosomal and subchromosomal…

A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples.

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CNVrd
Desktop

CNVrd

A read depth-based method to detect and genotype complex common copy number…

A read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data. CNVrd uses next-generation sequencing data to measure human gene copy number…

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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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GAIA
Desktop

GAIA Genomic Analysis of Important Alterations

Allows to find recurrent copy number alterations (CNAs). The GAIA method uses a…

Allows to find recurrent copy number alterations (CNAs). The GAIA method uses a discrete representation of the data to perform a permutation test. With it, a novel iterative procedure taking into…

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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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fastMitoCalc
Desktop

fastMitoCalc

Estimates Mitochondrial DNA (mtDNA) copy number highly accurately using 0.1% of…

Estimates Mitochondrial DNA (mtDNA) copy number highly accurately using 0.1% of the genome. fastMitoCalc is an application that takes advantage of the indexing of sequencing alignment files, focusing…

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Magnolya
Desktop

Magnolya

Enables copy number variation (CNV) detections without using a reference…

Enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets.

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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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SeqCNV
Desktop

SeqCNV

Uses capture next-generation sequencing (NGS) data. SeqCNV identifies the copy…

Uses capture next-generation sequencing (NGS) data. SeqCNV identifies the copy number ratio and copy number variant (CNV) boundary by extracting the read depth information and utilizing the maximum…

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GenomeCAT
Desktop

GenomeCAT

Allows analysis and integrative visualization of copy number variants (CNVs).…

Allows analysis and integrative visualization of copy number variants (CNVs). GenomeCAT is a standalone application that provides comprehensive tools for the analysis of DNA CNVs. The software…

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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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QDNAseq
Desktop

QDNAseq

A robust, cost-effective WGS method for DNA copy number analysis. The genome is…

A robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous…

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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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GENSENG
Desktop

GENSENG

A read-depth-based method that uses a hidden Markov model and negative binomial…

A read-depth-based method that uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the…

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HadoopCNV
Desktop

HadoopCNV

Infers copy number changes through both allelic frequency and read depth…

Infers copy number changes through both allelic frequency and read depth information. HadoopCNV enables multiple compute nodes to work in parallel. It is at least 6 times faster than CNVnator in term…

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Canvas
Desktop

Canvas

A tool for identification of copy number changes from diverse sequencing…

A tool for identification of copy number changes from diverse sequencing experiments including whole-genome matched tumor-normal and single-sample normal re-sequencing, as well as whole-exome matched…

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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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CopySeq
Desktop

CopySeq

A computational approach that analyzes the depth-of-coverage of high-throughput…

A computational approach that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to…

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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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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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XCAVATOR
Desktop

XCAVATOR

Discovers genomic regions involved in copy number variants (CNVs) from whole…

Discovers genomic regions involved in copy number variants (CNVs) from whole genome sequencing (WGS) data. The XCAVATOR method assists user in the identification and prediction of the absolute number…

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PopSV
Desktop

PopSV

Enables the systematic detection of Copy-Number Variations (CNVs) across the…

Enables the systematic detection of Copy-Number Variations (CNVs) across the genome. PopSV is an analytical method which detects abnormal read coverage using a set of samples as references. The…

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PureCN
Desktop

PureCN

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status…

Estimates tumor purity, copy number, loss of heterozygosity (LOH), and status of single nucleotide variants (SNVs). PureCN is designed for targeted short read sequencing data, integrates well with…

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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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TIGRA
Desktop

TIGRA

A computer program that conducts targeted local assembly of structural variants…

A computer program that conducts targeted local assembly of structural variants (SV) using targeted iterative graph routing assembly algorithm. Using data from the 1000 Genomes Project, TIGRA was…

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m-HMM
Desktop

m-HMM

A methodology for detecting CNVs based on a hidden Markov model with emission…

A methodology for detecting CNVs based on a hidden Markov model with emission probabilities that are governed by mixture distributions.

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ADM-CNV
Algorithm

ADM-CNV

Identifies copy number variations (CNVs) from raw next-generation sequencing…

Identifies copy number variations (CNVs) from raw next-generation sequencing (NGS) profiles. ADM-CNV is a method that formulates the read-depth (RD) signal reconstruction problem into a quadratic…

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COFFEE
Desktop

COFFEE COntrol-Free noninvasive FEtal chromosomal Examination

Allows fetal chromosomal aneuploidy testing in such a way that neither control…

Allows fetal chromosomal aneuploidy testing in such a way that neither control samples nor selection of genomic regions are required. COFFEE can be applied to various types of sequencing data. This…

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iCNV
Desktop

iCNV integrated Copy Number Variation caller

Allows copy number variation (CNV) detection. iCNV can be applied in whole…

Allows copy number variation (CNV) detection. iCNV can be applied in whole exome sequencing (WES) only, whole genome sequencing (WGS) only, single-nucleotide polymorphism (SNP) array only, or any…

BCIP
Dataset

BCIP Breast Cancer Integrative Platform

Maintains multi-omics data selected with strict quality control and processed…

Maintains multi-omics data selected with strict quality control and processed with uniform normalization methods. BCIP is a database that provides a user-friendly interface integrating comprehensive…

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modSaRa
Desktop

modSaRa

Detects chromosome copy number variants with high sensitivity and specificity.…

Detects chromosome copy number variants with high sensitivity and specificity. For a sequence of intensity values, the modified SaRa will process it by quantile normalization, search for change-point…

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PSE-HMM
Desktop

PSE-HMM

A tool for the genome-wide Copy Number Variation (CNV) detection from Next…

A tool for the genome-wide Copy Number Variation (CNV) detection from Next Generation Sequencing data (mate pair reads). PSE-HMM applies a Hidden Markov Model (HMM) with Position-Specific Emission…

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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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SRBreak
Desktop

SRBreak Split-read and Read-depth based Breakpoints

Identifies approximate breakpoints in the detection of copy-number variable…

Identifies approximate breakpoints in the detection of copy-number variable regions (CNVRs). SRBreak combines read-depth and split-read information to infer breakpoints, using information from…

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GROM-RD
Desktop

GROM-RD

Analyzes multiple biases in read coverage to detect CNVs in NGS data. To…

Analyzes multiple biases in read coverage to detect CNVs in NGS data. To overcome a typical weakness of read depth (RD) methods, GROM-RD employs a CNV search using size-varying overlapping windows to…

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MATCHCLIP
Desktop

MATCHCLIP

A method that identifies the breakpoints of a CNV using both the positions and…

A method that identifies the breakpoints of a CNV using both the positions and CIGAR strings of the reads that cover breakpoints of a CNV. In case the two break points of a CNV are in repeated…

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CNVPanelizer
Desktop

CNVPanelizer

Permits the utilization of a collection of non-matched normal tissue samples.…

Permits the utilization of a collection of non-matched normal tissue samples. CNVPanelizer employs a non-parametric bootstrap subsampling of the available reference samples to identify the…

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scoreInvHap
Desktop

scoreInvHap

Offers samples' inversion status of known inversions. scoreInvHap includes…

Offers samples' inversion status of known inversions. scoreInvHap includes genotype frequencies in the different haplotypes, R2 between the region of single nucleotide polymorphisms (SNPs) and…

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SCoNEs
Desktop

SCoNEs Somatic Copy Number Estimator

Estimates the Copy Number Variation (CNV) in whole genome sequencing (WGS)…

Estimates the Copy Number Variation (CNV) in whole genome sequencing (WGS) paired cancer data. SCoNEs uses a read depth approach. The software aims to decipher the general LRR signal in set of…

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QuicK-mer
Desktop

QuicK-mer

A unified pipeline for estimating genome copy-number from high-throughput…

A unified pipeline for estimating genome copy-number from high-throughput Illumina sequencing data. QuicK-mer utilizes the Jellyfish application to efficiently tabulate counts of predefined sets of…

TAGCNA
Desktop

TAGCNA

Identifies SCEs in somatic CNAs that may encompass cancer driver genes. TAGCNA…

Identifies SCEs in somatic CNAs that may encompass cancer driver genes. TAGCNA employs a peel-off permutation scheme to generate a reasonable null distribution based on a prior step of selecting tag…

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GWCNV
Desktop

GWCNV

Detects CNV associations with diseases through a genome-wide algorithm. GWCNV…

Detects CNV associations with diseases through a genome-wide algorithm. GWCNV is a genome-wide algorithm for detecting CNV associations with diseases. It works directly on a transformation of…

SVS
Desktop

SVS SNP and Variation Suite

Allows to perform complex analyses and visualizations on genomic and phenotypic…

Allows to perform complex analyses and visualizations on genomic and phenotypic data. SVS provides a set of tools to (1) empower quickly and easily perform quality-assurance and statistical tests for…

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CopyCat
Desktop

CopyCat

Detects copy number aberrations by measuring the depth of coverage obtained by…

Detects copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. CopyCat achieves higher accuracy than many other packages, and runs quickly…

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CNValidator
Desktop

CNValidator

Identifies high quality CNVs based on the density of homozygous SNPs and the…

Identifies high quality CNVs based on the density of homozygous SNPs and the ratio of heterozygous SNP reads. Using a rigorous statistical model, CNValidator will compute two test statistics and…

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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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