SeqWare

SeqWare

Developer(s)	SeqWare development team
Initial release	December 11, 2009 (2009-12-11) (0.3.0)
Discontinued	1.1.2  (November 18, 2015 (2015-11-18)) [±]
Preview release	[±]
Written in	Java
Operating system	Cross-platform
Type	Laboratory informatics software
License(s)	GNU General Public License v3
Website	seqware.github.io

SeqWare was a free open-source suite of software tools designed to act as a framework for building analysis workflows using the analysis tools you choose to implement. The software was targeted primarily at entities needing to analyze massive genomics datasets, especially those generated from next-generation sequencing (NGS) platforms.

Product history

Internal development on SeqWare — as an upgrade over existing software tools — began in roughly late 2007 or early 2008, primarily by Brian O'Connor of the Department of Human Genetics, University of California - Los Angeles. Release dates of early versions up to 0.3 aren't clear, but on December 11, 2009, those early versions were publicly released on an associated Google Project site. In early 2010, it was revealed SeqWare's new updates would play an important role in "transitioning the UCLA lab from being a microarray core to a second-generation sequencing core." SeqWare in particular would morph "to address a functionalities gap ... between vendor tools and those from sequencer manufacturers, and to offer a combination of workflow management, sample tracking, data storage, and data-querying possibilities." Work progressed steadily, including a 2012 switch from SourceForge to GitHub.

As of May 2021, no work has been performed on the project for over five years. The project is presumably abandoned.

The following table shows the dates of releases up to 0.12.1. Some dates may be approximate. For the release history from 0.12.5 to the current release, consult the release notes:

Version Release date 0.12.1 Unknown 0.12.0 Unknown 0.11.4 11 May 2012 0.11.2 Unknown 0.10.2 Unknown 0.10.1 Unknown 0.10.0 12 January 2012 0.9.1 Unknown 0.9.0 Unknown 0.8.0 Unknown

Version Release date 0.7.0 03 May 2010 0.6.1 24 February 2010 0.6.0 19 February 2010 0.5.0 18 February 2010 0.4.0 14 January 2010 0.3.0 11 December 2009 (public) 0.2.0 11 December 2009 (public) 0.1.2 11 December 2009 (public) 0.1.1 11 December 2009 (public)

Features

Features of SeqWare included:

• a database for storing metadata
• sample management
• data analysis and retrieval
• worflow management
• extensibility
• query

Hardware/software requirements

Requirements for proper installation of SeqWare included:

• a 64-bit Linux environment
• VirtualBox (if willing to run a local VM on Windows or MacOS)

More information about installation can be found on the GitHub site.

Videos, screenshots, and other media

Screenshots were provided in the user tutorial as well as much of the current documentation.

Entities using SeqWare

Current users included:

Lineberger Comprehensive Cancer Center, Nimbus Informatics

Further reading

• O'Connor, Brian D.; Merriman, Barry; Nelson, Stanley F. (2010). "SeqWare Query Engine: storing and searching sequence data in the cloud". BMC Bioinformatics 11 (Suppl. 12): S2. doi:10.1186/1471-2105-11-S12-S2. http://www.biomedcentral.com/1471-2105/11/S12/S2. 

• Marx, Vivien (5 February 2010). "UCLA Team Sequences Cell Line, Puts Open Source Software Framework into Production" (PDF). BioInform - Genomeweb LLC. http://pegasus.isi.edu/publications/ucla-pegasus.pdf. Retrieved 02 October 2012. 

External links

• SeqWare on Google Projects (deprecated)
• SeqWare GitHub repository (current)