Dear all,
I am currently working on the functional diversity of soil metagenomes. I have performed EggNOG annotations and would like to analyze the diversity and composition based on enzyme commission (EC) numbers, COG categories, and KEGG orthologs.
Although I have explored several workflows available on GitHub, most of them do not fully address my research question or are not tailored for diversity analysis.
If anyone is working on a similar topic or has experience with functional profiling using EggNOG output, I would greatly appreciate it if you could share your analysis workflow, relevant tools, or scripts that helped you with functional diversity and compositional analysis.
Thank you in advance for your support.
Best regards,
Balamurugan sadaiappan
Balamurugan Sadaiappan , To analyze functional diversity from EggNOG annotations, first extract EC numbers, COG categories, and KEGG orthologs from the .emapper.annotations file using tools like eggnogCOGextractor or custom scripts. Then, build an abundance table (functions vs. samples). Use R packages like vegan to calculate diversity indices (Shannon, Simpson) and visualize with ggplot2 or pheatmap. For functional enrichment, you can use the FunFEA package. This approach allows you to assess both diversity and functional composition across your soil metagenomes.
