Number of reads per species present in an in-house simulated ocean metagenome compared to the number of reads assigned to a reference containing all known strains by Genometa.

<p>All bacterial species present were detected. Reads were retrieved in the same stoichiometric proportions in which they were inserted. <i>Halobacterium</i> sp NRC-1 was also detected, but this strain is colinear and practically identical to the included strain <i>Halobacterium salinarum</i> R1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041224#pone.0041224-Pfeiffer1" target="_blank">[29]</a>.</p

Number of reads from an artifical metagenome of known composition (SimLC dataset; [<b>19</b>]) which were included in the metagenome (black bars) and assigned to the correct bacterial species by Genometa (blue bars).

<p>Only the top 21 species of the 113 bacteria included in the dataset are shown. Genometa achieves a high accuracy on this dataset. Asterisks indicate strains which are included in the SimLC dataset but not in the Genometa reference sequence. Inter strain differences generally mean less reads are attributed to these taxa. The cross denotes a species which is not present in the Genometa reference sequence.</p

A screenshot displaying key new features with a glacier ice metagenome dataset loaded [<b>39</b>].

<p>An aligner can be run with the graphical dialogue (top right) against a reference sequence. Thereafter the resulting file format is converted to the standard BAM format and read in, revealing the number of reads mapped to each species in a sortable list which can be exported for further analysis (left). A bar graph graphically displays the number of reads attributed to each taxon. Clicking on a blue bar takes the user to a genome level view of the distribution of reads mapped against a taxon. Large datasets can thus be easily aligned, analysed and tested for plausibility from a graphical user interface.</p

The number of 100,000 Illumina human gut 100 bp reads (SRR042027, Human Microbiome Project, [17]) assigned to bacterial species by four metagenomic programs.

<p>Note the general agreement between the different programs but higher number of read assignments achieved by Genometa and MG-RAST. All programs found bacterial species typical of a human gut metagenome.</p

Software recommendations for analysis of different types of metagenome datasets.

<p>Software recommendations for analysis of different types of metagenome datasets.</p

Comparative duration of alignment by BLAST and Bowtie versus the same metagenomic reference for four metagenome datasets.

*<p>duration was extrapolated after ∼24 hours.</p