EUKulele is a Python program for taxonomic annotation of microbes in metatranscriptomic and metagenomic samples, with special emphasis on eukaryote discovery. EUKulele can be downloaded from PyPI, or it may be downloaded via conda and used as a command-line program. The software includes four major features:
- Database setup and formatting
- Database creation, alignment, and taxonomic estimation
- Assessment of the BUSCO completeness of subsets of contigs at each taxonomic level
- Assessment of taxonomic classification using only BUSCO-identified core eukaryotic genes
In principle, there are two prerequisites for running the software:
- Metagenomic or metatranscriptomic sample files (unless using the provided sample data)
- A database to align the contigs from the metagenome/metatranscriptome to
Three databases are supported by default from within EUKulele, and may be downloaded and formatted automatically if the user chooses (or if another reference directory is not specified/does not exist):
If installed either with pip or conda, EUKulele can be invoked via::
EUKulele <arguments>
Where the minimal command would be
EUKulele --mets_or_mags <choice of data type> --sample_dir <where samples are located>
See the documentation for further details.
If you are interested in modifying EUKulele, you may fork the project for your own use, as detailed in the MIT License we have adopted for the project. In order to contribute, please contact the developers via Arianna Krinos (akrinos (at) mit (dot) edu) after making the desired changes, after which a pull request may be submitted.
If you have any suggestions for feature additions or any problems with the software that you would like addressed with the development community, please submit an issue on the Issues tab of the project GitHub repository. You may want to search the existing issues before submitting, to avoid asking a question or requesting a feature that has already been discussed.
If you have questions about how to use EUKulele, or would like to seek out collaborations related to this project, you may contact Arianna Krinos at akrinos (at) mit (dot) edu.
Authors: Arianna Krinos, Sarah Hu, Natalie Cohen, and Harriet Alexander.