BioTechniques (May 2005)

Management and visualization of whole genome shotgun assemblies using SAM

  • René L. Warren,
  • Yaron S. Butterfield,
  • Ryan D. Morin,
  • Asim S. Siddiqui,
  • Marco A. Marra,
  • Steven J.M. Jones

DOI
https://doi.org/10.2144/05385ST01
Journal volume & issue
Vol. 38, no. 5
pp. 715 – 720

Abstract

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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.