REFRESH Bioinformatics Group

CoMeta

CoMeta—What is it?

CoMeta (Classification of metagenomes) is a tool used to assigns a query read (DNA fragment) from metagenomic sample into one of the groups (the most common the taxon).

The architecture of CoMeta

CoMeta is composed of several programs (written in Perl and C++ language) that were used in our experiments on metagenomic data sets.

Terms of use of CoMeta

CoMeta is in general a free compression program available in both binary and source code releases. More details can be found out on download page.

Publications

+ Kawulok, J., Deorowicz, S., CoMeta: Classification of Metagenomes Using k-mers, PLOS ONE, 2015; 10(4):1–23, Abstract.

Nowadays, the study of environmental samples has been developing rapidly. Characterization of the environment composition broadens the knowledge about the relationship between species composition and environmental conditions. An important element of extracting the knowledge of the sample composition is to compare the extracted fragments of DNA with sequences derived from known organisms. In the presented paper, we introduce an algorithm called CoMeta (Classification of metagenomes), which assigns a query read (a DNA fragment) into one of the groups previously prepared by the user. Typically, this is one of the taxonomic rank (e.g., phylum, genus), however prepared groups may contain sequences having various functions. In CoMeta, we used the exact method for read classification using short subsequences (k-mers) and fast program for indexing large set of k-mers. In contrast to the most popular methods based on BLAST, where the query is compared with each reference sequence, we begin the classification from the top of the taxonomy tree to reduce the number of comparisons. The presented experimental study confirms that CoMeta outperforms other programs used in this context. CoMeta is available at https://github.com/jkawulok/cometa under a free GNU GPL 2 license.