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 larger than 1 kbp.

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,…

Desktop app
G T A T C G C T A Control-FREEC Control-FREEC

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…

Desktop app
G T A T C G C T A CNVnator CNVnator

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…

Desktop app
G T A T C G C T A RDXplorer RDXplorer

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…

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 WIthin-SamplE COpy… WIthin-SamplE COpy Number aberration DetectOR

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.

Desktop app
G T A T C G C T A Copy number… Copy number estimation by a Mixture Of PoissonS

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…

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 CNV-seq CNV-seq

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…

Desktop app
G T A T C G C T A Geometric Analysis of… Geometric Analysis of Structural Variants

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…

Desktop app
G T A T C G C T A JointSLM JointSLM

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…

Desktop app
G T A T C G C T A readDepth readDepth

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…

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 GENSENG GENSENG

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…

Desktop app
G T A T C G C T A CopySeq CopySeq

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…

Desktop app
G T A T C G C T A Magnolya Magnolya

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.

Desktop app
G T A T C G C T A GenomeCAT GenomeCAT

GenomeCAT

Offers a broad spectrum of visualization and analysis tools that assist in the…

Offers a broad spectrum of visualization and analysis tools that assist in the evaluation of copy number variants (CNVs) in the context of other experiment data and annotations. GenomeCAT, a…

Desktop app
G T A T C G C T A PureCN PureCN

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…

Desktop app
G T A T C G C T A BIC-seq BIC-seq

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…

Desktop app
G T A T C G C T A Split-read and… Split-read and Read-depth based Breakpoints

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…

Desktop app
G T A T C G C T A GWCNV GWCNV

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…

Desktop app
TAGCNA TAGCNA

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…

Web app
G T A T C G C T A Architecture Querying… Architecture Querying Podium

Aquerium Architecture Querying Podium

Visualizes genomic presence and absence of biomolecules with a focus on protein…

Visualizes genomic presence and absence of biomolecules with a focus on protein domain architectures. Aquerium offers advanced domain organization querying against the database of pre-computed…

Desktop app
G T A T C G C T A PSE-HMM PSE-HMM

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…

Desktop app
G T A T C G C T A TrioCNV TrioCNV

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…

Desktop app
G T A T C G C T A Canvas Canvas

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…

Desktop app
G T A T C G C T A QuicK-mer QuicK-mer

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…

Desktop app
G T A T C G C T A GROM-RD GROM-RD

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…

Desktop app
G T A T C G C T A modSaRa modSaRa

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…

Desktop app
G T A T C G C T A QDNAseq QDNAseq

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…

Desktop app
G T A T C G C T A CopyCat CopyCat

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…

Desktop app
G T A T C G C T A TIGRA TIGRA

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…

Desktop app
G T A T C G C T A CNVrd2 CNVrd2

CNVrd2

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. CNVrd2 uses next-generation sequencing data to measure human gene copy…

Desktop app
G T A T C G C T A m-HMM m-HMM

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.

Desktop app
G T A T C G C T A MATCHCLIP MATCHCLIP

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…

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 micro-read Copy… micro-read Copy Number Variant Regions

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…

Desktop app
G T A T C G C T A CNValidator CNValidator

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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