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Research Article

SAM-Profiler: A Graphical Tool for Qualitative Profiling of Next Generation Sequencing Alignment Data

Flora Francesco1, Pirola Alessandra2, Spinelli Roberta2, Redaelli Sara2, Valletta Simona2, Gambacorti Passerini Carlo2 and Piazza Rocco2*

1Department of Informatics, Systems and Communication, University of Milano-Bicocca, 20900, Monza, Italy

2Deptartment of Health Sciences, University of Milano-Bicocca, 20900, Monza, Italy

*Corresponding Author:
Piazza Rocco
Department of Health Sciences
University of Milano-Bicocca
20900, Monza, Italy
Tel: 0390264488059
Fax: 0390264488363
E-mail: [email protected]

Received date: July 25, 2013; Accepted date: August 15, 2013; Published date: August 22, 2013

Citation: Francesco F, Alessandra P, Roberta S, Sara R, Simona V, et al. (2013) SAM-Profiler: A Graphical Tool for Qualitative Profiling of Next Generation Sequencing Alignment Data. J Comput Sci Syst Biol 6:188-193. doi:10.4172/jcsb.1000116

Copyright: © 2013 Francesco F, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License,which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


SAM/BAM alignment file formats are extensively used in virtually all the laboratories devoted to high-throughput sequencing. However, limited effort has been yet dedicated to the development of SAM/BAM quality reporting tools. To overcome this problem, we developed SAM-Profiler, a multiplatform tool dedicated to the advanced quality reporting of SAM/BAM files. SAM-Profiler performs qualitative analysis of SAM/BAM alignment data in the context of next-generation sequencing. It is implemented in C# and can be run under Windows, Linux and MacOS operative systems. Two versions are available: fully graphical, event-driven software and a command-line tool. SAM-Profiler is able to generate an extensive set of qualitative reports on SAM/BAM alignment data, among them: overall, per-base and per-chromosome read quality, mapping quality, duplicate and coverage analyses, bases distribution, perfect, proper and improper mapping, exonic, intronic, intergenic, 5` and 3` UTR coverage, mismatch distribution profile and CG distribution. In presence of paired-end sequencing experiments our tool is able to automatically report the insert size distribution and to analyze the relative pair mapping, reporting absolute and relative distribution of properly, improperly mapped, mapped/unmapped and unmapped pairs. Its modular architecture allows embedding additional analytical monitoring/reporting tools to the already developed list, allowing SAM-Profiler to grow according to the specific requests of the end-users.


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