What is FunOMIC?

While analysis of the bacterial microbiome has become routine, that of the fungal microbiome, namely mycobiome, is still hampered by the lack of robust fungal databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic and functional databases for the identification of fungi in shotgun metagenomic sequencing data.


FunOMIC-T: database for taxonomic mycobiome profiling that includes more than 1.6 million fungal single-copy marker genes
FunOMIC-P: database for functional mycobiome profiling that includes more than 3 million fungal protein sequences
BacterialDB: database for removing bacterial reads before mycobiome profiling

User instruction:

Please find the user guide in FunOMIC

Citing FunOMIC

If you use FunOMIC, please cite:

Xie, Z. and Manichanh, C. (2022). FunOMIC: Pipeline with built-in Fungal Taxonomic and Functional Databases for Human Mycobiome Profiling. https://doi.org/10.1016/j.csbj.2022.07.010

As well as all third-party tools used by the pipeline.