The concept of the CLC Microbial Genomics
The CLC Microbial Genomics includes tools for microbial community analysis as well as tools for epidemiological typing of microbial isolates.
Microbiome composition analysis based on 16S rRNA and other commonly used metagenome derived amplicon data is fully supported, including tools for i) automatic downloading of reference databases (Greengenes, SILVA and UNITE), ii) OTU clustering, iii) taxonomy assignment iv) rarefaction and diversity estimation and v) cross-sample comparisons using PERMANOVA and PCoA. Chimeric sequences are automatically detected during the OTU clustering step. The primary output of the clustering, tallying and taxonomic assignment processes is an OTU table, listing the abundances of OTUs in the samples under investigation viewable through a number of intuitive visualization options. Secondary analyses include estimations of alpha and beta diversities, in addition to statistical tests for differential abundance.
For epidemiological typing of microbial isolates using NGS data, tools for NGS-MLST typing and identification of antimicrobial resistance genes as well as automatic downloading of reference databases and MLST schemes are in place. In cases when the precise identity of the isolated species is not known, the tool automatically detects the most closely related reference genome in NCBI's RefSeq bacterial genome collection and the corresponding MLST scheme from MLST.net or PubMLST.org. The powerful new CLC metadata framework allows the fast and intuitive browsing, sorting, filtering and selection of samples and associated metadata, including results obtained during analysis. This metadata framework provides a dashboard-like overview for easy filtering and selection of samples for other analyses such as k-mer or SNP tree reconstruction and visualisation for outbreak analysis.
For convenience, expert-configured workflows for microbiome analysis as well as epidemiological typing allow the user to get from raw NGS reads through data processing and statistical analysis to the final graphical results in as few as four steps.