1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
    1. Overview
    2. Building and Installing
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics

SeqWare Portal


This web application is used to track the processing of SeqWare sequence data through the SeqWare-supplied pipeline, alignment to a reference genome, and report generation.

It is part of the larger SeqWare project that looks to streamline the manipulation of sequence data produced by next gen sequencers. The SeqWare LIMS system is closely tied with the SeqWare Pipeline software that controls the actual processing, alignment, and annotation of sequence data. SeqWare LIMS collects various bits of metadata related to each flowcell and lane used in the sequencer and passes this information via a common database backend to the SeqWare Pipeline software.

Warning: The SeqWare Portal is not currently in production use and is unmaintained in favour of the command-line tools. We are currently working on a replacement so use at your own risk.

SeqWare Pipeline then records the status of each step in the processing pipeline back to the database. These “processing” messages are then displayed in the LIMS system. This makes it very easy for researchers to both follow the progress of a particular run and also get back to the reports automatically created based on their initial settings.

See the User Guide for examples of how to use the Portal for setting up Samples, Experiments, Studies, and uploading data for use by workflows.

Building and Installing

Most users will want to use our pre-configured VMs, see the SeqWare Install Guide for how to get the VM. Please see the Install Guide for building and installing the SeqWare Portal.