STAMP Users Guide

User Manual:

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Page | 1   STAMP User’s Guide v1.08 Statistical Analysis of Metagenomic Profiles  Donovan Parks and Robert Beiko  March 13, 2011 Contents 1.  Introduction ........................................................................................................................................................2 2.  Contact information ...........................................................................................................................................2 3.  Citing STAMP ......................................................................................................................................................2 4.  Installation ..........................................................................................................................................................2 4.1 Precompiled binaries for Microsoft Windows ..............................................................................................2 4.2 Source code ..................................................................................................................................................3 4.3 Unit tests: Verifying the installation .............................................................................................................3 5.  Analyzing metagenomic profiles ........................................................................................................................3 5.1 Obtaining and constructing metagenomic profiles ......................................................................................3 5.2 Configuring metagenomic profiles for analysis ............................................................................................5 5.3 Exploratory analysis ......................................................................................................................................5 5.4 Statistical techniques in STAMP ...................................................................................................................8 5.5 Filtering results .......................................................................................................................................... 10 5.6 Statistical plots........................................................................................................................................... 11 5.7 Saving plots and tables .............................................................................................................................. 13 5.8 Global preferences .................................................................................................................................... 13 5.9 Empirical tests: Confidence interval coverage and power analysis .......................................................... 14 6.  Command-line interface .................................................................................................................................. 14 7.  Custom statistical techniques and plots .......................................................................................................... 15 7.1 Creating a custom plot .............................................................................................................................. 16 7.2 Making a plugin publicly available ............................................................................................................. 17 8.  References ....................................................................................................................................................... 17
Page | 2   1. Introduction STAMP (STatistical Analysis of Metagenomic Profiles) is a software package for analyzing metagenomic profiles, such as a phylogenetic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways. It aims  to  promote  ‘best  practices’  in  choosing  appropriate  statistical  techniques  and  in  reporting  results  by encouraging the use of effect sizes and confidence intervals for assessing biological importance. A user-friendly, graphical interface permits easy exploration of statistical results and generation of publication-quality plots for inferring the biological relevance of features in a metagenomic profile. STAMP is open-source, extensible via a plugin framework, and available for all major platforms. This  document  provides  a  tutorial  style  introduction  demonstrating  how  STAMP  can  be  used  to  analyze metagenomic profiles. Functional profiles for the obese and lean mouse microbiomes originally investigated by Turnbaugh et al. (2006) is used to illustrate the use of STAMP. 2. Contact information STAMP is in active development and we are interested in discussing all potential applications of this software. We  encourage you  to  send  us  suggestions for  new  features.  Suggestions,  comments,  and  bug  reports can  be sent to Rob Beiko (beiko [at] cs.dal.ca). If reporting a bug, please provide as much information as possible and a simplified version of the data set which causes the bug. This will allow us to quickly resolve the issue.  3. Citing STAMP If you use STAMP in your research, please cite the following article:  Parks, D.H. and Beiko, R.G (2010). Identifying biologically relevant differences between metagenomic communities. Bioinformatics, 26, 715-721. 4. Installation 4.1 Precompiled binaries for Microsoft Windows A precompiled binary is available for Microsoft Windows. This binary has been tested under Windows XP and Windows 7,  but should  also work under Windows Vista.  The precompiled  binary  is available  from the STAMP website: http://kiwi.cs.dal.ca/Software/STAMP If  you  have  a  pristine  copy  of  Microsoft  Windows  installed  you  may  need  to  install  the  Visual  C++  2008 Redistributable Package: Windows XP or x86 (32-bit) versions of Windows Vista or 7 x64 (64-bit) versions of Windows Vista or 7

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