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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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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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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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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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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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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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FACETS
Desktop

FACETS Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing

An allele-specific copy number analysis (ASCN) tool and open-source software…

An allele-specific copy number analysis (ASCN) tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms. FACETS provides a…

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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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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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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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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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ACEseq
Desktop

ACEseq Allele-specific copy number estimation with whole genome sequencing

Allows users to detect copy number aberrations (CAN) on cancer whole genome…

Allows users to detect copy number aberrations (CAN) on cancer whole genome sequencing (WGS) data. ACEseq provides an automated platform without prior information requirement. The software can…

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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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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…

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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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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…

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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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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