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

Download the latest version of SmashCommunity.

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