SeqWare is an open-source bioinformatics workflow deployment and management system. Its core features include:
You would want to use SeqWare in order to build workflows and processes that automate large volumes of NGS analysis, that track analytical events in a database (provenance), and that link analysis to wet lab entities like samples and studies. You would especially want to use SeqWare if you needed to do the above on both a local and cloud-based environments or if you have a lot of different types of clusters to submit jobs to.
You would not want to use SeqWare if you have a small number of NGS samples to analyze, if you need to interactively explore tools and settings for your project, or you want pre-built workflows that will analyze data “out-of-the-box”. If this is you, we would instead recommend you look for commercial solutions such as Nimbus Informatics, DNAnexus, or BaseSpace for pre-built workflows ready to run on the cloud or Galaxy for interactive analysis either locally or on the cloud. Remember, SeqWare is an infrastructure toolkit not an analysis pipeline for particular NGS experimental designs. You use SeqWare to build the workflows you need.
The type of users targeted by the SeqWare project are ones that have massive amounts of NGS data to analyze (TBase to PBase), have specific/custom analytical workflows in mind, that their workflows are typically more complex than the generic workflows offered by other projects, want to automate and track analysis of their data, and need to be able to run on a local cluster or the cloud.
There are currently 3 different ways to work with SeqWare:
There are several workflow engines which can be used for NGS data analysis: Ergatis, Galaxy, Pegasus and Taverna. Each has their own strengths and weaknesses depending on how easy they are to work with vs. how much data they can process. Some of these provide ready-made workflows for analyzing NGS data while others require you to build your own. There are also commercial solutions available on the cloud that typically provide a one-size-fits all model in which they have a collection of standardized workflows that a user can choose from. Examples include BaseSpace by Illumina, DNAnexus and Samsung SDS Bioinformatics Service. These commercial services attempt to accomplish similar things to a SeqWare install but they offer the analysis itself as a service whereas SeqWare allows you to create local or cloud-based infrastructure similar to what powers these commercial offerings.