SAM - Sequence Assembly Manager

SAM is a Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type.

Project Description

Summary

SAM consists primarily of a MySQL relational database and Perl applications designed to easily manipulate and coordinate the analysis of genomic information and to view and report genome assembly progress through its CGI web interface. The application includes a tool to compare sequence assemblies to fingerprint maps, used successfully to improve and validate both maps and sequence assemblies of the Rhodococcus sp. RHA1 genome.

Main Features

Some of the key features of SAM include:

• Execution, Storage, Visualization, Analysis and Manipulation of Whole Genome Shotgun (WGS) Assemblies
• Fast Assessment of Assembly Progress and Quality
• Assembly Comparisons
• Validation of Sequence Assemblies and Fingerprint Maps
• High Throughput Quality Control of WGA
• Automated Platform for Gene Prediction and Annotation
• Central Repository for Storing Assembly, Analyses, Annotation & Finishing Information
• Eases the Use of External Programs Through its Web Interface

Requirements

SAM requires Perl, BioPerl and MySQL,and runs on Linux. SAM's usefulness is optimal when used in conjunction with Phrap, Arachne and Glimmer.

Documentation

The installation and run-me files are available for download and bundled up with the software.

A powerpoint presentation (January 8th, 2004) serves as an introduction to key concepts and algorithms behind SAM.

Warren RL, Butterfield YS, Morin RD, Siddiqui AS, Marra MA, Jones SJM. (2005) Management and Visualization of Whole Genome Shotgun Assemblies using SAM. Biotechniques. 38:715-720

Credits

Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones
Funding Provided by Genome BC.