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.
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 genetic association studies, (2) perform genetic prediction including various means of defining the relationship between samples, (3) validate models and visualize the results, (4) identify regions of copy number variability, (5) perform statistical tests on the copy number results and others.
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.
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.
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.
Affords a way for analysis of Pacific Biosciences long-read sequencing data. PBSuite is composed of two projects: PBJelly and PBHoney. The first one is an automated pipeline for aligning long sequencing reads to draft assembles. The second provides identification approaches for analyze high mappability of long reads considering intra red discordance and soft-clipped tails.