Graph-based tools for metagenomics data analysis
Metagenomics studies communities of microorganisms inhabiting various environmental niches such as soil, water, human skin and gut. The analysis of metagenomic samples using classical genomic approaches like assembly and annotation is limited due to the size and complexity of sample and limited number of curated reference genomes. At CTLab we develop graph-based computational tools for reference-free analysis of metagenomes. The first tool to present is MetaFast — a toolkit for analysis of metagenomic samples based on de Bruijn graph examination . We discuss several pipelines, including comparative analysis of lake water samples and application of a tool for Inflammatory Bowel Diseases diagnosis. The second tool MetaCherchant provides a researcher with a convenient way to find and track selected sequences (e.g. antibiotic resistance genes) in metagenomic samples . We will also tell a few words about our recent article on analysis of metagenome time series after Fecal Microbiota Transplantation using the RECAST tool .