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 larger than 1 kbp.
A statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data. BCFtools can manipulate variant calls in the variant call format (VCF) and its binary counterpart BCF. It also can discover somatic and germline mutations with appropriate input data, efficiently estimate site allele frequency, allele frequency spectrum and linkage disequilibrium, and test Hardy–Weinberg equilibrium and association.
Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
Finds copy number variations (CNVs) from a statistical analysis of mapping density of short reads from next-generation sequencing platforms. CNVnator separates the whole genome into non-overlapping bins of equal size and utilizes the count of mapped reads within each bin as the read-depth (RD) signal. It can be useful for the study of various human and nonhuman genomes.
Retrieves balanced and unbalanced forms of structural variation, such as deletions, tandem duplications, inversions and translocations. DELLY is based on a combination of short-range and long-range paired-end mapping and split-read analysis. It is useful for massively parallel sequencing (MPS) data from various sources, including deep whole-genome sequencing data and low-pass mate-pair sequencing data with longer inserts.
Automatically detects copy number alterations (CNAs) and loss of heterozygosity (LOH) regions using next-generation sequencing (NGS) data. Control-FREEC consists of three steps: (i) calculation and segmentation of copy number profiles, (ii) calculation and segmentation of smoothed BAF profiles; and (iii) prediction of final genotype status. The software can call genotype status including when no control experiment is available and/or the genome is polyploid. It also corrects for GC-content and mappability biases.
Offers a solution for analyzing desktop sequencing data produced by the Roche Junior, Illumina MiSeq or ION PGM™. NextGENe is a program that includes analysis modules for: copy number variation (CNV), alternate splicing of exons and transcript expression levels, single nucleotide polymorphism (SNP)/INDEL and structural variant analysis (resequencing and Amplicon analysis), prediction and rare disease discovery, as well as whole genome alignment or transcriptome.
Provides a validated, single framework for off-instrument data analysis for a wide variety of Next Generation Sequencing (NGS) applications. SOLiD BioScope Software provides a command line and simple web interface for running application-specific sequence analysis tools. It enables user to perform off-instrument secondary and tertiary analyses. It also allows configurable bioinformatics workflows for resequencing (mapping, Single Nucleotide Polymorphism (SNP) finding (DiBayes), Human copy number variations, inversions, small indels, large indels), ChIP-Seq, and whole transcriptome analysis (mapping, fusion/splicing, counting, UCSC WIG Files creation).