Local analysis

Discover the power of spatial omics with local analysis on your workstation or compute cluster!

Analysis of sequencing data generated with the Trekker Single-Cell Spatial Mapping Kit and the Seeker Spatial Transcriptomics Kit can be done using either cloud analysis or your local workstation or compute cluster. For more information on cloud analysis, refer to the Cloud analysis page.

Takara Bio provides bioinformatics tools for spatial bioinformatics on a local system. The flexibility of a local solution provides users with:

• On-premises data storage and governance
• Offline analysis capabilities
• Control of hardware and software configurations
• Avoidance of recurring cloud compute or storage costs

Local analysis requires both a Linux platform (≥256 GB RAM and 12 cores) and the Trekker or Seeker Primary Analysis Pipeline software. See below for more information about the pipelines.

Trekker Bioinformatics Solution

The Trekker Primary Analysis Pipeline processes sequenced data by extracting single nuclei barcodes from FASTQ Read 1 and spatial barcodes from FASTQ Read 2, then assigns spatial locations to each nucleus through barcode matching. Upon completion, it produces a QC metrics report along with files compatible with the downstream Secondary Data Analysis Workflow. To get started, visit our Trekker Bioinformatics Solution page.

Seeker Bioinformatics Solution

The Seeker Primary Analysis Pipeline processes sequenced data to reconstruct a spatial map of gene expression for secondary analyses. It requires paired end FASTQ files and a reference genome for the species surveyed. Upon completion, it produces a QC metrics report along with files compatible with the downstream Secondary Data Analysis Workflow. To get started, contact Technical Support at technical_support@takarabio.com.