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Latest improvements for QIAGEN OmicSoft Suite

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QIAGEN OmicSoft Suite

Release date: 2020-04-16

QIAGEN OmicSoft Suite 2020 R1 Release notes

A new version of QIAGEN OmicSoft Suite has been released. Please review the latest improvements and update your OmicSoft Server at the next available opportunity to take advantage of these new features included in version 10.2.7!

  • Array Suite is now OmicSoft Suite! This is purely a name change to reflect the wide variety of Omics data supported by OmicSoft.
    • OmicSoft Studio=Array Studio. OmicSoft Server=Array Server. OmicSoft Viewer=Array Viewer.

Figure 1. New name change of Array Studio as OmicSoft Studio, as part of OmicSoft Suite.

  • Support for Docker images and cloud analysis with External Scripts improvements
    • OmicSoft Suite now supports External Scripts on AWS Cloud, and can run analyses on Docker images.
      These new capabilities substantially expand the options for QIAGEN OmicSoft Suite as an ‘omics data and analysis hub, allowing advanced users who would like to run third-party bioinformatics tools to do so from OmicSoft Suite, and even build pipelines to analyze data and import into OmicSoft projects. Talk with your account manager to learn more about some of the possibilities, or check out these links.
  • Improvements to single-cell preprocessing (oscript only)
    • Single-cell preprocessing (non-10x) now supports cell barcode correction, matching the 10x preprocessing function’s capability of “fuzzy” matching to cell barcode white lists
    • 10x preprocessing and non-10x preprocessing oscript support /DeleteSkippedReads and /ExportSkippedReads options to manage output files
    • 10x and non-10x preprocessing functions will summarize the top reasons for skipped reads for each sample with /SummarizeSkippedReads
  • Server startup optimizations
    • DisableParallelLandLoading enforces Land Loading individually, instead of using all CPUs specified with CPUNumber in ArrayServer.cfg
  • Improved BAM CIGAR handling
    • SAM/BAM reads that contain ‘=’ or ‘X’ will be loaded and reads will be displayed
    • “Validate SAM/BAM” will validate files that contain a read with ‘=’ or ‘X’

Software maintenance to consider:

Additional details on major improvements:

Docker support and cloud support for External Scripts

With version 10.2.1 we are proud to support for Docker images in “External Scripts”. This is considered an advanced feature for OmicSoft “power-users” who want to extend their OmicSoft Suite capabilities beyond tools integrated into the software. Because of the wide variety of tools that can run in Docker images, OmicSoft Support cannot provide debugging support for each tool, but will be happy to answer questions about External Scripts syntax, provide tutorials and example scripts. The QIAGEN Discovery Services team can also work with you to build full pipelines and workflows using External Scripts and Docker images for a variety of bioinformatics needs.

To support External Scripts on AWS, you will need to use an updated AMI. Please visit http://www.arrayserver.com/wiki/index.php?title=Build_AWS_Ubuntu_AMI_for_OmicSoft_Cloud_Computing

To support Docker in External Scripts on your onsite OmicSoft Server installation, please install Docker v19.

More useful resources:

A full log of all the changes is located in the Help menu of the Analysis tab in OmicSoft Studio. To download this log, click here: