Alignment-free Methods for Classification of Metagenomic Data
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Metagenomics studies microbial communities by analyzing their genomic content directly sequenced from the environment. In this contribution, alignment-free methods based on word frequency will be introduced. It has been proven, that these methods are effective in processing of short metagenomic sequence reads produced by Next-Generation Sequencing technologies. To evaluate the potential of word frequency based methods, the k-mer analysis was applied on simulated dataset of metagenomic sequence reads with length of 600 nucleotides. Then the data were enrolled for a hierarchical cluster analysis. Results have shown that the proposed method is able to cluster genome fragments of the same taxa.
Document typePeer reviewed
Document versionxmlui.vut.verze.Publishers's version
SourceProceedings of the 22nd Conference STUDENT EEICT 2016. s. 244-246. ISBN 978-80-214-5350-0
- Student EEICT 2016