1 - 8 of 8 results

IGV / Integrative Genomics Viewer

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Enables users to explore large, integrated genomic datasets. IGV provides next-generation sequencing (NGS) data visualization and provides features for identification of sequencing and analysis artifacts, leading to errant single-nucleotide variant (SNV) calls, as well as support for viewing large-scale structural variants (SV) detected by paired-end read technology. The software also includes features to support third-generation long-read sequencing technologies. Several IGV features have been developed to aid manual review of aligned reads.


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A software tool for copy number detection that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines.


A free software tool for copy number variation (CNV) detection from SNP genotyping arrays. PennCNV can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs from segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.


Enables tightly integrated comparative variant analysis and visualization of thousands of next generation sequencing (NGS) data samples and millions of variants. BasePlayer is a highly efficient and user-friendly software for biological discovery in large-scale NGS data. It transforms an ordinary desktop computer into a large-scale genomic research platform, enabling also a non-technical user to perform complex comparative variant analyses, population frequency filtering and genome level annotations under intuitive, scalable and highly-responsive user interface to facilitate everyday genetic research as well as the search of novel discoveries.


A software tool for normalized visualization, statistical scoring, and annotation of CNVs from population-scale whole-genome sequencing (WGS) datasets. CNView has six sequential steps: (1) matrix filtering, (2) matrix compression, (3) intra-sample normalization, (4) inter-sample normalization, (5) coverage visualization, and (6) genome annotation. CNView surmounts challenges of sequencing depth variability between individual libraries by locally adapting to cohort-wide variance in sequencing uniformity at any locus. Importantly, CNView is broadly extensible to any reference genome assembly and most current WGS data types.


A user-friendly tool with functions specifically designed to facilitate the process of interactively visualizing and editing somatic CNV calling results. Different from other general genomics viewers, the index and display of CNV calling results in cnvCurator is segment central. It incorporates multiple CNV-specific information for concurrent, interactive display, as well as a number of relevant features allowing user to examine and curate the CNV calls. cnvCurator provides important and practical utilities to assist the manual review and edition of results from a chosen somatic CNV caller, such that curated CNV segments will be used for down-stream applications.

VCS / Visualization of CNV or SNP

Provides a graphical view of the physical distribution of Copy number variation (CNV) or single nucleotide polymorphism (SNP) on chromosomes. VCS is an online application that shows the enrichment genome contents in region having specific range like: gene, long interspersed nuclear element [LINE], short interspersed nuclear element [SINE], long terminal repeat [LTR], simple repeat, low complexity, miRNA, tRNA, CpG island, and Gene Ontology - Biological Process, Molecular Function, and Cellular Component.