In silico mock communities for evaluation of taxonomic profilers across eukaryotes in the human microbiome

In silico mock communities generated with CAMISIM for benchmarking the performance of taxonomic profilers across prokaryotic (50 communities), eukaryotic (30 communities), and viral communities (10 communities) of the human microbiome. Metagenomes were generated using CAMISIM (Fritz et al., 2019), which simulates 2.1 Gb of Illumina 2 ×150 bp paired end reads with the default HiSeq 2500 error profile and a mean insert size of 200 bp.

Eukaryotic communities30 eukaryotic in silico metagenomes comprising up to 200 randomly sampled genomes from a set of 113 eukaryotic species (See Supplementary Table 2 from the paper) corresponding to the eukaryotic species within both CHAMP and MetaPhlAn 4 (Blanco-Míguez et al., 2023) databasess.

Prokaryotic and viral communities

In silico data for prokaryotic and viral communities from the human microbiome can be found here: doi: 10.5281/zenodo.10777404

References

Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., et al. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology 2023 41:11 41, 1633–1644. doi: 10.1038/s41587-023-01688-w

Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., et al. (2019). CAMISIM: Simulating metagenomes and microbial communities. Microbiome 7, 1–12. doi: 10.1186/S40168-019-0633-6/FIGURES/5