High-throughput sequencing software tools > Whole-genome sequencing software tools
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.
An algorithm for the correct alignment of two nucleotide sequences containing SVs, i.e.…
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 modification of the alignment scoring scheme(s) that is…
Combines normalization of the data at the nucleotide level and Bayesian information…
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 the first version in 2011 used a control genome…
A Perl/C++ package that provides genome-wide detection of structural variants from next…
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 base pairs to 1 megabase pair that are difficult…
A tool for identification of copy number changes from diverse sequencing experiments…
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 and unmatched tumor-normal studies. In addition…
A method to detect copy number variation using shotgun sequencing. The method is based on…
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 essential confidence values for detection of CNV.
Identifies high quality CNVs based on the density of homozygous SNPs and the ratio of…
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 their corresponding p-value estimates for each CNV…
An approach to discover, genotype, and characterize typical and atypical CNVs from family…
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 (86%-96%), low false-discovery rate (3%-20%), high…
A read depth-based method to detect and genotype complex common copy number variants from…
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 number for multiple samples, identify SNPs tagging copy…
A data processing pipeline for copy number variations and aberrations (CNVs and CNAs)…
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 matrices or genomic ranges objects, which are the…
Detects copy number aberrations by measuring the depth of coverage obtained by massively…
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 by utilizing multi-core architectures to…
A computational approach that analyzes the depth-of-coverage of high-throughput DNA…
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 infer locus copy-number genotypes. CopySeq can…
A tool for genome assembly and variation analysis from sequence data. You can use it to…
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, you can use Cortex to look specifically for…
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 effects of multiple confounders. Based on extensive…
A tool for identifying structural variants (SVs) from paired-end sequencing data. GASV is…
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 represents the uncertainty in measurement of a…
Analyzes multiple biases in read coverage to detect CNVs in NGS data. To overcome a…
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 improve breakpoint resolution. GROM-RD was able…
An algorithm that extend the univariate SLM to the multivariate case in order to detect…
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 the signal to noise ratio (SNR) of the data:…
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.
Enables copy number variation (CNV) detections without using a reference genome. Magnolya…
Enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares two next-generation sequencing datasets.
A method that identifies the breakpoints of a CNV using both the positions and CIGAR…
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 regions and the break points are not unique, MATCHCLIPS…
A copy number caller that analyzes the whole-genome next-generation sequence mapping read…
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 absolute copy numbers of genomic intervals.
Detects chromosome copy number variants with high sensitivity and specificity. For a…
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 candidates, eliminate unlikely change-points, and…
A computational framework with simulation-based error models for inferring genomic…
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 workflow, SV-Simulation and BreakDB. PEMer workflow is a…
Detects breakpoints of large deletions, medium sized insertions, inversions, tandem…
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 uses a pattern growth approach to identify the…
A robust, cost-effective WGS method for DNA copy number analysis. The genome is divided…
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 two-dimensional loess correction for sequence…
A unified pipeline for estimating genome copy-number from high-throughput Illumina…
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 k-mers. The program performs GC-normalization using…
A computational tool for copy number variants (CNV) detection in whole human genome…
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 read depth coverage is estimated in…
This package for R can detect copy number aberrations by measuring the depth of coverage…
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 does not require the sequencing of a reference…
Detects structural variants from targeted short-DNA reads. Both real and simulated data…
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 well as translocations and viral integration sites…
A computer program that conducts targeted local assembly of structural variants (SV)…
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 able to accurately assemble the majority of deletion…
A tool designed to jointly detecting copy number variations (CNVs) from whole genome…
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 to accommodate over-dispersion and considered GC…
A tool for discovery of structural variation in one or more individuals simultaneously…
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 conflict resolution mechanism that no longer…
A set of python scripts that detects fetal chromosomal and subchromosomal duplications…
A set of python scripts that detects fetal chromosomal and subchromosomal duplications and deletions in maternal blood samples.
