Download the human gut metagenome data associated with the enterotypes article

Download enterotype data

Posted on apr 20, 2011

Processed metagenomic reads
Metagenomic reads have been processed to remove human contamination, sequencing vector/adapter and low quality sequences.
bundled, individual
Assembled contigs
Processed metagenomic reads assembled using Arachne v3.1.
bundled, individual
Predicted genes and proteins
Genes predicted using GeneMark v1.6p.
bundled, individual
Functional annotations of predicted proteins
Predicted proteins annotated using eggNOG orthologous groups.
bundled, individual
Genus and phylum abundance tables of the three datasets
bundled, individual
Functional abundance table for the Sanger dataset
orthologous groups

Keywords: raw data, contigs, genes, annotations, phylogenetic, functional

Download SmashCommunity

Posted on apr 20, 2011

Download the latest version of SmashCommunity.

Keywords: SmashCommunity

Microbial reference genomes used in the enterotypes article

Posted on Apr 20, 2011

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.

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

Keywords: genomes, draft, assembly, reference sequences