This repository contains all scripts, documents and information related to the evaluation of six bioinformatic tools for their ability to classify fungal genomes. The following tools were evaluated:
EukDetect: Lind, A.L., Pollard, K.S. Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing. Microbiome 9, 58 (2021). https://doi.org/10.1186/s40168-021-01015-y
FindFungi: Donovan, P. D., Gonzalez, G., Higgins, D. G., Butler, G., & Ito, K. (2018). Identification of fungi in shotgun metagenomics datasets. PloS one, 13(2), e0192898. https://doi.org/10.1371/journal.pone.0192898
FunOMIC: Xie Z, Manichanh C. FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling. Comput Struct Biotechnol J. 2022 Jul 11;20:3685-3694. https://doi.org/10.1101/2022.05.09.491154
HumanMycobiomeScan: Soverini, M., Turroni, S., Biagi, E. et al. HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples. BMC Genomics 20, 496 (2019). https://doi.org/10.1186/s12864-019-5883-y
Kraken 2: Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0
MetaPhlAn3: Beghini, F. et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife 10, e65088 (2021). https://doi.org/10.7554/eLife.65088
MetaPhlan4: Blanco-Míguez, A., Beghini, F., Cumbo, F. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol 41, 1633–1644 (2023). https://doi.org/10.1101/2022.08.22.504593
The evaluation was performed by Arfa Irej Qureshi for her Masters thesis during the academic year 2022/2023. The thesis is available at https://www.duo.uio.no/handle/10852/104186.
Disclaimer: The evaluation of EukDetect and MetaPhlAn4 was performed in February and January 2024, respectively, and thusly not included in the Master thesis.