Install SmashCommunity on your system. This sections walks you through the installation of SmashCommunity and setting up external software.

This is the best way to get a feel for SmashCommunity. This tutorial walks you through the analysis of a sample metagenomic dataset using SmashCommunity. You add the data to the repository, run the basic steps in the annotation procedure and run the analysis scripts to understand the data.

Learn all the options and modes of the annotation and analysis scripts that are part of SmashCommunity. Although the tutorial shows you how to analyze a dataset, knowing the functionalities of the scripts helps you customize the analysis to your data.

Here's an overview of the analysis scripts.

Here you find detailed information on each analysis script.

This section lists some common metagenomic analysis tasks that are not performed using the default workflow in SMASH. It deals with advanced installation, using external data, parallelizing BLAST runs efficiently on a cluster, using the batch mode of SMASH, using the matrix/hash manipulation routines and comparative analysis among others.

Commonly asked questions.

Learn all the options and modes of the annotation and analysis scripts that are part of SmashCommunity. Although the tutorial shows you how to analyze a dataset, knowing the functionalities of the scripts help you customize the analysis to your data.