On 2013 Nov 01, Stephen Turner commented:

Genometa is a computationally efficient software for bacterial species identification from high-throughput short-read metagenomic sequencing data. Older tools for sequence identification required longer read lengths or genome assembly for species identification. Newer tools are capable of community profiling without assembly. However, tools like MEGAN (Huson DH, 2007) rely on basic local alignment search tool (BLAST) searching, which is computationally demanding. Genometa uses the Bowtie aligner, which is orders of magnitude faster. The authors tested the method against a simulated low-complexity dataset and found that Genometa is highly accurate when query species are included in the reference database (otherwise it performs poorly, as would be expected). This software including a graphical user interface is freely available.

On 2013 Nov 01, Stephen Turner commented:

Genometa is a computationally efficient software for bacterial species identification from high-throughput short-read metagenomic sequencing data. Older tools for sequence identification required longer read lengths or genome assembly for species identification. Newer tools are capable of community profiling without assembly. However, tools like MEGAN (Huson DH, 2007) rely on basic local alignment search tool (BLAST) searching, which is computationally demanding. Genometa uses the Bowtie aligner, which is orders of magnitude faster. The authors tested the method against a simulated low-complexity dataset and found that Genometa is highly accurate when query species are included in the reference database (otherwise it performs poorly, as would be expected). This software including a graphical user interface is freely available.