LabKey Server provides data management and workflow automation for DNA sequencing and genotyping experiments. Using LabKey Server, you can:

• Manage and build dictionaries of reference sequences, including associated sample and run-specific information.
• Import and manage genotyping data: reads, quality scores, metadata, and metrics.
• Analyze reads directly in LabKey Server or export to FASTQ files for use in other tools.
• Initiate genotyping analyses using Galaxy. LabKey sends selected reads, sample information, and reference sequences to Galaxy, and uses the Galaxy web API to load this data into a new Galaxy data library.
• Automatically import results when the Galaxy workflow is complete.
• Store large Illumina sequence data as files in the file system, with links to sample information and ability to export subsets of sequencing data.

Supported Instruments

The genotyping tools are designed to support import, management, and analysis of sequencing data from:

• Roche 454 instruments (GS Junior and GS FLX)
• Illumina instruments (for example, MiSeq Benchtop Sequencer)
• PacBio Sequencer by PacBio Systems

We are currently expanding sequencing support to include new instruments and new analysis methods. We are always interested in partnering with institutions who want to contribute to this effort. Contact us to join this effort.

Documentation

• Set Up a Genotyping Dashboard
• Example Workflow: LabKey and Galaxy - Manage sequencing resources and interactions with a Galaxy server using data from a Roche 454 Sequencer.
• Example Workflow: LabKey and Illumina - Manage sample and sequencing results from an Illumina MiSeq Benchtop Sequencer.
• Example Workflow: LabKey and PacBio - Import and manage sequencing results from a PacBio Sequencer.
• Example Workflow: O'Connor Module - Perform enhanced experiment management using the O'Connor module.
• Import Haplotype Assignment Data - Import existing haplotype assignment information for integration with other data.
• Work with Haplotype Assay Data - Generate a report of haplotype assignments (and discrepancies).

Resources

• Contact LabKey for more information about these capabilities.