1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  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


Amazon Web Services (AWS)
A cloud provider, Amazon provides on demand instances and storage and is the cloud system on which we deploy SeqWare.
A template system for Java’s build system Maven. We use it in SeqWare as a template tool to quickly generate new Workflow Bundles, Modules, etc.
FreeMarker template language (FTL)
A simple markup language for Java previously used by our older, legacy workflow engine.
High Performance Computing (HPC)
A term that describes traditional cluster compute environments common at Universities and large research organizations.
Indivisible Unit of Sequence (IUS)
A term to describe de-multiplexed sequence from a sequencer run.
The SeqWare MetaDB tracks both experimental events (studies, samples, experiments, etc) and computational events (workflows, workflow runs, and processing events).
Loosely based on MIME types, a unique identifier that describes the format of the file produced by a SeqWare Pipeline workflow.
An API for steps in a workflow. Can be used to extend the SeqWare system by core developers. Most workflow developers will simply use the BashJob to run command line tools as steps in workflows.
Next Generation Sequencing (NGS)
A collection of high-throughput sequencing technologies.
Processing Event
Information about individual steps in a workflow are saved in the MetaDB using the processing table.
Sequencer Run
The Sequencer Run table in the MetaDB stores information about physical runs of the sequencer.
Virtual Machine (VM)
A virtualized OS running on another machine. We use VirtualBox to redistribute SeqWare for use locally and an AMI for use on Amazon’s cloud.
Workflow Bundle
A zip file (using Zip64) that contains the workflow definition, binary files, data files, etc. Everything that needs to be included to run the workflow.
Workflow Engine
There are two main sets of workflow engines in SeqWare 1) Oozie and 2) Whitestar. The first uses the Hadoop system for running jobs while the second is a group of workflow engines that can run workflows directly for debugging purposes.
Workflow Run
Represents a run of a given workflow in the MetaDB.
More To Come…
We will add more in the near future, please suggest terms you would like defined in the comments section below.