SmashCommunity

SmashCommunity

SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It comes with built-in support for state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction, and can be easily extended to support additional software. SmashCommunity provides tools to estimate the quantitative phylogenetic and functional compositions of metagenomes, compare compositions of multiple metagenomes and produce intuitive visual representations of such analyses.
Visit the downloads section to download the latest version.

Keywords: metagenomics, iTOL

SmashCommunity v1.6 available!

Posted on Apr 20, 2011; Updated on Sep 09, 2011

SmashCommunity v1.6 includes several months worth of improvements, bugfixes, new features and optimizations. We know, there was never a v1.5, but that is because v1.5 was an internal release and it progressed so much that we are at v1.6. Starting from v1.6, SmashCommunity supports functional annotation of metagenomes using the KEGG functional database, which organizes genes at the orthologous group, functional module and functional pathway levels. Check the image on the left to see the nature of functional information that you can obtain using annotations with the KEGG database.

Download SmashCommunity v1.6p2

Minor update on Sep 09, 2011

There was a minor update to v1.6 on Sep 09 that fixes the URL for meta_rna/rRNA_hmm software, so that the installation process does not stall. If you had trouble installing the older v1.6 package, please download the latest version. The latest version is v1.6p2.
Note: KEGG functional database is not free anymore. We are working on ways to let the users download KEGG database file by themselves and then install support for KEGG functional annotation. We hope to get this fixed by the end of September 2011.
Please see "Applying a patch" in Special Topics to learn how to upgrade to the newest patch.

Minor update on May 06, 2011

There was a minor update to v1.6 on May 06

• fixing a couple of bugs related to functional analysis,
• adding an easy option to use MySQL as the database of choice.

If you choose MySQL as the database of choice, a MySQL database containing information about reference genomes and reference proteins will also be downloaded now, which may take some time. Please see "Applying a patch" in Special Topics to learn how to upgrade to the newest patch.

Key Features in this version:

1. functional annotation using the KEGG functional database
2. ability to make your own reference genome database or reproduce what we make available (requires BioPerl to be installed)
3. several new visualization of results:
   1. ability to visualize functional compositions of metagenomes on iTOL and browse through additional annotation information
   2. improved phylogenetic mapping of the microbial reference sequences to the RDP taxonomic tree by identifying the 16S rRNA gene sequences from them
   3. ability to analyze metagenomic sequences in the RDP taxonomic tree space and display the results on iTOL, either on the NCBI or on the RDP tree
   4. ability to analyze 16S sequences in the RDP taxonomic tree space and display the results on iTOL, either on the NCBI or on the RDP tree

Special thanks to:

Ivica Letunic, EMBL/BioByte

For making the coolest tree visualization tool, iTOL, and for adding so many features that SmashCommunity uses to display phylogenetic and functional summaries of metagenomic samples,

Takuji Yamada, EMBL

For the KEGG information digest (proteins, KOs, modules, pathways) and the contribution to several quantitative procedures,

Les Dethlefsen, Stanford

For being a patient beta tester and providing valuable feedback in making v1.6 stable,

Daniel R. Mende, EMBL

For being the longest standing beta tester since Smash was actually in beta stage and the contribution to several quantitative prodecures,

Jens Roat Kultima, EMBL

For being a beta tester and finding errors in the website,

Rest of Bork group, EMBL

For moral support.

See the downloads section for older versions.

Keywords: metagenomics, KEGG, iTOL

SmashCommunity v1.4.1 available!

Posted on Sep 20, 2010

SmashCommunity v1.4.1 adds support to MetaGeneMark, a flavor of GeneMark that is optimized for metagenomic data.
Get yourself a copy of the latest version from the downloads section.

SmashCommunity v1.4 available!

Posted on July 26, 2010

SmashCommunity v1.4 takes away all the complications of installing a complex analysis pipeline and lets the user do what he/she intends to do: metagenomic analysis. Agreed, the older versions of SmashCommunity demanded more efforts from users to install external software used by SmashCommunity as well as installing SmashCommunity itself. Those days are gone! If you have installed a GNU tool on your linux machine before, you know all you need to know to install SmashCommunity.

./configure --prefix=/home/nobody/smash
make
make install
      

Get yourself a copy of the latest version from the downloads section.
Check out the installation manual to see for yourself how easy it is to install and see the tutorial to start using it right away.

SmashCommunity v1.3 available!

Posted on May 20, 2010

The latest version of SmashCommunity includes several tools for comparative metagenomic analysis. It uses the iTOL batch access API to generate tree-based visualization of results.
The following sequence assemblers are supported:

1. Arachne
2. Celera Assembler

The following microbial gene predictors are supported:

1. GeneMark
2. MetaGeneAnnotator

The latest version of SmashCommunity includes the following technical features:

• support for raw SFF files from 454 technology
• support for the Celera assembler

Visit the downloads section to download the latest version.