EUKulele
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes - Published in JOSS (2021)
Science Score: 95.0%
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Found 1 DOI reference(s) in JOSS metadata -
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Published in Journal of Open Source Software
Scientific Fields
Repository
Automatic eukaryotic taxonomic classification
Basic Info
- Host: GitHub
- Owner: AlexanderLabWHOI
- License: mit
- Language: Python
- Default Branch: master
- Size: 81 MB
Statistics
- Stars: 28
- Watchers: 4
- Forks: 7
- Open Issues: 22
- Releases: 13
Metadata Files
README.md
EUKulele
Formalizing environmental eukaryotic taxonomic assignment
About EUKulele
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
Prerequisites for running EUKulele
In principle, there are two prerequisites for running the software: 1. Metagenomic or metatranscriptomic sample files (unless using the provided sample data) 2. 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):
- PhyloDB
- EukProt
- MMETSP
Basic usage
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.
Community guidelines
How to contribute to EUKulele
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.
Submitting an issue
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.
Asking for help
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.
Acknowledgments
Authors: Arianna Krinos, Sarah Hu, Natalie Cohen, and Harriet Alexander.
Owner
- Name: Alexander Lab @ WHOI
- Login: AlexanderLabWHOI
- Kind: organization
- Email: halexander@whoi.edu
- Location: Woods Hole, MA
- Website: AlexanderLabWHOI.github.io
- Repositories: 17
- Profile: https://github.com/AlexanderLabWHOI
JOSS Publication
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
Authors
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, MIT-WHOI Joint Program in Oceanography, Cambridge and Woods Hole, MA, USA
Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
Editor
Will Rowe
Tags
Taxonomy Metagenomics MetatranscriptomicsGitHub Events
Total
- Create event: 1
- Release event: 1
- Issues event: 7
- Watch event: 1
- Issue comment event: 24
- Push event: 4
Last Year
- Create event: 1
- Release event: 1
- Issues event: 7
- Watch event: 1
- Issue comment event: 24
- Push event: 4
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| akrinos | a****s@v****u | 281 |
| Harriet Alexander | h****r@g****m | 53 |
| shu251 | s****u@w****u | 2 |
| ARIANNA KRINOS | a****s@p****r | 2 |
| Natalie Cohen | n****n@w****u | 1 |
| Johannes Werner | j****r@u****e | 1 |
| Arfon Smith | a****n | 1 |
| Will Rowe | w****e@b****k | 1 |
| ARIANNA KRINOS | a****s@p****r | 1 |
| ARIANNA KRINOS | a****s@p****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 55
- Total pull requests: 14
- Average time to close issues: about 1 year
- Average time to close pull requests: about 21 hours
- Total issue authors: 31
- Total pull request authors: 5
- Average comments per issue: 3.35
- Average comments per pull request: 0.43
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: 2 days
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 4.67
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- susheelbhanu (7)
- halexand (7)
- akrinos (6)
- jolespin (3)
- cnatalie (3)
- danilodileo (3)
- paulzierep (2)
- johanneswerner (1)
- michoug (1)
- nvpatin (1)
- slaperriere (1)
- saky7009 (1)
- qfaber (1)
- luciazifcakova (1)
- blsteven (1)
Pull Request Authors
- akrinos (10)
- arfon (1)
- johanneswerner (1)
- halexand (1)
- will-rowe (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 36 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 16
- Total maintainers: 1
pypi.org: eukulele
A package to make the process of taxonomically classifying microbial eukaryotes easier.
- Homepage: https://github.com/AlexanderLabWHOI/EUKulele
- Documentation: https://eukulele.readthedocs.io/
- License: MIT
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Latest release: 2.1.2
published 8 months ago
Rankings
Maintainers (1)
Dependencies
- ipykernel *
- nbsphinx *
- argparse *
- biopython *
- chardet *
- joblib *
- matplotlib *
- multiprocess *
- numpy *
- pandas *
- pytest-cov *
- pytest-xdist *
- python-coveralls *
- pyyaml *
- seaborn *
- sphinxcontrib-bibtex ==1.0.0
- ujson *
- wget *