Management and visualization of whole genome shotgun assemblies using SAM. (May 2005)

• Record Type: Journal Article
• Authors: Warren, René L.; Butterfield, Yaron S.; Morin, Ryan D.; Siddiqui, Asim S.; Marra, Marco A.; Jones, Steven J.M.
• Is Part Of: Biotechniques. Volume 38:Number 5(2005)
• Page Start: 715
• Page End: 720
• Publication Date: 2005-05
• Subjects: Biology, Experimental -- Periodicals; Molecular biology -- Periodicals; Medical technology -- Periodicals; Biology, Experimental; Medical technology; Molecular biology; Clinical Laboratory Techniques -- Periodicals; Research -- Periodicals; Medical Laboratory Science -- Periodicals; Periodicals; Electronic journals; 570
• DOI: 10.2144/05385ST01
• Languages: English
• ISSNs: 0736-6205

Abstract

We have designed and implemented a system to manage whole genome shotgun sequences and whole genome sequence assembly dataflow. The Sequence Assembly Manager (SAM) consists primarily of a MySQL relational database and Perl applications designed to easily manipulate and coordinate the analysis of sequence information and to view and report genome assembly progress through its Common Gateway Interface (CGI) web interface. The application includes a tool to compare sequence assemblies to fingerprint maps that has been used successfully to improve and validate both maps and sequence assemblies of the Rhodococcus sp. RHA1 and Cryptococcus neoformans WM276 genomes.