SeqWare
| Developer(s) | SeqWare development team |
|---|---|
| Initial release | December 11, 2009 (0.3.0)[1] |
| Stable release |
1.1.2 (November 18, 2015) [±] |
| Preview release | [±] |
| Written in | Java |
| Operating system | Cross-platform |
| Type | Laboratory informatics software |
| License(s) | GNU General Public License v3 |
| Website | seqware.github.com |
SeqWare is 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 is 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.[2][3] 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.[1] 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."[2] 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."[2] Work progressed steadily, including a 2012 switch from SourceForge to GitHub.[4]
The following table shows the dates of various releases. Some dates may be approximate:
| Version | Release date | ||
|---|---|---|---|
| 0.1.1 | 11 December 2009 (public)[1] | ||
| 0.1.2 | 11 December 2009 (public)[1] | ||
| 0.2.0 | 11 December 2009 (public)[1] | ||
| 0.3.0 | 11 December 2009 (public)[1] | ||
| 0.4.0 | 14 January 2010[1] | ||
| 0.5.0 | 18 February 2010[1] | ||
| 0.6.0 | 19 February 2010[1] | ||
| 0.6.1 | 24 February 2010[1] | ||
| 0.7.0 | 03 May 2010[5] | ||
| 0.8.0 | Unknown[6] | ||
| 0.9.0 | Unknown[6] | ||
| 0.9.1 | Unknown[6] | ||
| 0.10.0 | 12 January 2012[4] | 0.10.1 | Unknown[6] |
| 0.10.2 | Unknown[6] | ||
| 0.11.2 | Unknown[6] | ||
| 0.11.4 | 11 May 2012[4] | ||
| 0.12.0 | Unknown[7] | ||
| 0.12.1 | Unknown[7] | ||
| 0.12.5 | 6 August 2012[8] | ||
| 0.13.0 | 20 August 2012[8] | ||
| 0.13.1 | 03 September 2012[8] |
Features
Features of SeqWare include[3]:
- a database for storing metadata
- sample management
- data analysis and retrieval
- worflow management
- extensibility
- query
Hardware/software requirements
Requirements for proper installation of SeqWare include:
- 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 are provided in the user tutorial as well as much of the current documentation.
Entities using SeqWare
Current users include[9]:
Lineberger Comprehensive Cancer Center, Nimbus Informatics, Ontario Institute for Cancer Research
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 SourceForge (deprecated)
- SeqWare on Google Projects (deprecated)
- SeqWare GitHub repository (current)
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 "trunk/seqware-queryengine/backend/dist/ - SeqWare". Google Project Hosting. http://code.google.com/p/seqware/source/browse/trunk/seqware-queryengine/backend/dist/?r=601. Retrieved 02 October 2012.
- ↑ 2.0 2.1 2.2 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.
- ↑ 3.0 3.1 "SeqWare - About". GitHub, Inc.. http://seqware.github.com/about/. Retrieved 02 October 2012.
- ↑ 4.0 4.1 4.2 "SeqWare - Main Page". SourceForge. 24 September 2012. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Main_Page. Retrieved 02 October 2012.
- ↑ "SeqWare - 20100426". SourceForge. 26 April 2010. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=20100426. Retrieved 02 October 2012.
- ↑ 6.0 6.1 6.2 6.3 6.4 6.5 "Setup SeqWare MetaDB - Upgrading your Database Version". SourceForge. 10 July 2012. http://sourceforge.net/apps/mediawiki/seqware/index.php?title=Setup_SeqWare_MetaDB#Upgrading_your_Database_Version. Retrieved 02 October 2012.
- ↑ 7.0 7.1 "BOConnor's Wiki - Research Blog". Brian O'Connor. https://boconnor.is-a-geek.com/pmwiki/index.php?n=Main.HomePage?logdate=201206. Retrieved 02 October 2012.
- ↑ 8.0 8.1 8.2 "SeqWare - Release Notes". GitHub, Inc.. http://seqware.github.com/release-notes/. Retrieved 02 October 2012.
- ↑ "SeqWare - Partners". Brian O’Connor. http://seqware.github.com/partners/. Retrieved 02 October 2012.
