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Biodiscovery Nexus Software

Description

Nexus Copy Number (BioDiscovery) is a graphical user interface (GUI) based bioinformatics software that specializes in copy number detection using array or sequence derived data. Its analysis capabilities are listed below.

List of Analysis Functions

Copy number analysis

  • Using array or sequence based data, the user can:
    • detect copy number variations at the individual and population level
    • identify subgroups in populations that show significant gains in copy number
    • detect gain or loss of heterozygosity
    • cluster samples that have similar patterns of variation
    • view results in a genomic context using genome browser
    • find molecular pathways that are affected by CNV
    • query databases such as The Cancer Genome Atlas (TCGA) to gain insight from existing data or integrate existing data with the user's own data

Recommendations

While Nexus Copy Number is a GUI based copy number analysis tool and does not require knowledge with scripting, it is a good idea to consult with bioinformatics experts at the Center for Cancer Research Collaborative Bioinformatics Resource (CCBR) who have in-depth experience in CNV analysis and know the limitations of various tools.

Things to Know

Nexus Copy Number runs on the user's machine so it may be limited by local resources. By default, Nexus Copy Number comes with human (NCBI build 36.1, 37) and mouse (NCBI build 38) reference genomes. Additional reference genomes for other organisms of interest are available here. Human build 38 can be downloaded from here. Newer genome builds may be created upon request by contacting BioDiscovery Technical Support.

Input Data Types

  • Nexus Copy Number can take data from various arrays as input including Affymetrix CEl. To see the full list, click on "Load" -> "Load Data" -> "Select data type".
  • For high throughput sequencing, users can input
    • BAM
    • VCF

Output Data Types

  • Analysis reports from Nexus Copy Number can be exported as TXT.
  • Visualizations can be exported as JPEG, PNG, TIFF, and SVG at various resolutions.

Access Information

This is an NCI-licensed software with a 2 concurrent use license. To access Nexus Copy Number, submit a request at service.cancer.gov.

Getting Help

For help with this package, see

Additional resources can be found under the Resources tab on the BioDiscovery website.