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Somatic copy-number alteration detection software tools | Whole-genome sequencing data analysis

Somatic copy-number alterations (SCNAs) are an important type of structural variation affecting tumor pathogenesis. Accurate detection of genomic regions with SCNAs is crucial for cancer genomics as these regions contain likely drivers of cancer…
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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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CONSERTING
Desktop
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Patchwork
Desktop

Patchwork

A bioinformatic tool for analyzing and visualizing allele-specific copy numbers…

A bioinformatic tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which…

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SynthEx
Desktop

SynthEx

Caters to the varying protocols of different next-generation sequencing…

Caters to the varying protocols of different next-generation sequencing protocols, to detect copy number alterations (CNAs). SynthEx uses a “synthetic-normal” strategy to correct for sample-specific…

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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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sCNAphase
Desktop

sCNAphase

An R package, designed for estimating tumor copy number profile, tumor…

An R package, designed for estimating tumor copy number profile, tumor cellularity, tumor ploidy, based on whole genome sequencing (WGS) or whole exome sequencing (WES) data. sCNAphase integrates…

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HMMcopy
Desktop

HMMcopy

A suite of tools to make copy number estimations for whole genome data with GC…

A suite of tools to make copy number estimations for whole genome data with GC and mappability correction, then segment and classify copy number profiles with a robust Hidden Markov Model. Designed…

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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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CalMaTe
Desktop

CalMaTe Calibration Matrix T

Normalizes allele-specific copy number estimates (ASCNs) from any technology…

Normalizes allele-specific copy number estimates (ASCNs) from any technology and preprocessing method, without requiring matched normal. CalMaTe is a platform-independent multi-array method that…

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iGC
Desktop

iGC

Identifies differentially expressed genes driven by Copy Number Alterations…

Identifies differentially expressed genes driven by Copy Number Alterations (CNA) from samples with both gene expression and CNA data. iGC supports multiple input formats and users can define their…

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HATS
Desktop

HATS Haplotype Amplification in Tumor Sequences

A tool that calls the amplified alleles, and thus amplified haplotype, in copy…

A tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next-generation sequencing tumor data. The amplified haplotype may reveal gene variants. We…

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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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CNAseg
Desktop

CNAseg

A framework for the identification of CNA events that uses flowcell-to-flowcell…

A framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls. HMMseg uses…

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AbsCN-seq
Desktop

AbsCN-seq

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers…

A simple and robust algorithm to infer purity, ploidy and absolute copy numbers in whole numbers for tumor cells from sequencing data. A simulation study shows that estimates have reasonable…

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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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WaveCNV
Desktop

WaveCNV

A software package to identify copy number alterations by detecting breakpoints…

A software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using…

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COPS
Desktop

COPS COpy number using Paired Samples

An accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs…

An accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from…

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OncoSNP-SEQ
Desktop

OncoSNP-SEQ

An analytical tool for characterizing copy number alterations and…

An analytical tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.

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Segmentum
Desktop

Segmentum

Segments the genome by analyzing the read-depth and B-allele fraction profiles…

Segments the genome by analyzing the read-depth and B-allele fraction profiles using a double sliding window method. Segmentum is a tool for the identification of copy number alterations (CNAs) and…

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seqCNA
Desktop

seqCNA

A parallelized R package for an integral copy number analysis of…

A parallelized R package for an integral copy number analysis of high-throughput sequencing cancer data. seqCNA includes novel methodology on (i) filtering, reducing false positives, and (ii) GC…

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rSW-seq
Desktop

rSW-seq

A method for identification of copy number alterations in a tumor genome…

A method for identification of copy number alterations in a tumor genome compared to its matched control, based on application of Smith-Waterman algorithm to single-end sequencing data. In a…

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CESAM
Desktop

CESAM Cis Expression Structural Alteration Mapping

Finds somatic copy-number alterations (SCNAs) mediating gene dysregulation in…

Finds somatic copy-number alterations (SCNAs) mediating gene dysregulation in cis by integrating SCNAs, expression and chromatin interaction domain data. CESAM employs statistical concepts from…

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VCF2CNA
Web

VCF2CNA

Detects copy number alteration (CNA). VCF2CNA is a web-based tool capable of…

Detects copy number alteration (CNA). VCF2CNA is a web-based tool capable of accurate and efficient detection of CNAs from variants called from high-coverage wide genome sequencing (WGS) data…

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SomatiCA
Desktop

SomatiCA

A package that is capable of identifying, characterizing and quantifying SCNAs…

A package that is capable of identifying, characterizing and quantifying SCNAs from cancer genome sequencing. By directly accounting for tumor purity and subclonality, SomatiCA was especially…

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CLImAT
Desktop

CLImAT CAN and LOH Assessment in Impure and Aneuploid Tumors

A bioinformatic tool for identification of genome-wide aberrations from tumor…

A bioinformatic tool for identification of genome-wide aberrations from tumor samples using whole-genome sequencing data.

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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…

Copy Number…
Desktop
Web

Copy Number Explorer

An interactive tool for mining large copy number datasets. Copy Number Explorer…

An interactive tool for mining large copy number datasets. Copy Number Explorer facilitates rapid visual and statistical identification of recurrent regions of gain or loss, identifies the genes most…

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