Download SmashCommunity v1.6p2.

This version includes several improvements.

Download SmashCommunity v1.4.1.

This version adds support to the MetaGeneMark gene prediction software.

Download SmashCommunity v1.4.

The latest version of SmashCommunity makes the deployment and use of the software as easy as it can be.

For the phylogenetic analysis of metagenomic samples, metagenomic reads are mapped to reference genomes using DNA sequence similarity. This requires a reference genome sequence database and the taxonomic information about these sequences in the database. See phylogenetic analysis section for more details.

Reference genomes v2.0 contains 5.16Gb from 1511 complete and draft microbial genomes obtained as follows:

1. Entrez Genome, using "archaea[organism] AND complete[PROP]"
2. Entrez Genome, using "bacteria[organism] AND complete[PROP]"
3. Human Microbiome Project DACC
4. MetaHIT Consortium

These were obtained on July 04, 2010 and have been preprocessed to be compatible with SmashCommunity.

 

Download the files essential for the reference genome based phylogenetic analysis:

1. Reference genome sequences
2. Smash formatted RefOrganismDB sqlite database
3. Smash formatted RefOrganismDB mysql database

Download Ubuntu 10.04 server (amd64) with pre-installed SmashCommunity and SmashCell.

You can test SmashCommunity's capabilities by running some tests on the virtual machine. And you avoid installing SmashCommunity yourself, if you just want to analyze a dataset only once.

Please use "ubuntu" for username and password.

Download SmashCommunity v1.3.

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 our tutorial section to learn how to install and use SmashCommunity. To run the steps in the analysis section of the tutorial, download the data available here. You could also use your own data in the tutorial.

Metagenomic sample data

sequences (36MB)

quality (64MB)

traceinfo (2MB)

tarball of above files (102MB)

Read mappings to reference genome set

blastn output

Gene mappings to eggNOG proteins

blastp output

For the phylogenetic analysis of metagenomic samples, metagenomic reads are mapped to reference genomes using DNA sequence similarity. This requires a reference genome sequence database and the taxonomic information about these sequences in the database. See phylogenetic analysis section for more details.

Reference genomes v1.0 contains 1152 complete and draft microbial genomes obtained from the following sources:

1. NCBI
2. Washington University
3. Baylor College of Medicine
4. Broad Institute
5. MetaHIT Consortium

These were obtained in May 2009 and have been preprocessed to be compatible with SmashCommunity.

 

Download the files essential for the reference genome based phylogenetic analysis:

1. Reference genome sequences
2. Taxonomic mapping of sequences

For the functional analysis of metagenomic samples, predicted genes are mapped to reference proteins from the eggNOG database using protein sequence homology. This requires access to the eggNOG protein sequence database and the orthology information about these sequences in the database. See functional analysis section for more details. The current version of eggNOG (v2.0) consists of 224,847 orthologous groups in 630 species, covering 2,242,035 proteins.

Download the files essential for the eggNOG based functional analysis:

1. Reference proteins: protein.sequences.v2.txt.gz from the "Downloads" section of eggNOG
2. Orthology mapping of reference proteins: this will be downloaded by SMASH automatically when you install

Note on Feb 09, 2011:

Starting from SmashCommunity v1.5, it is not necessary to download these files separately. The installer will automatically download it for you.