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Welcome to the Eukfinder Wiki Page.
For detailed documentation and comprehensive guides, please refer to our User Manual.
- Running Eukfinder with Illumina short reads
- Running Eukfinder with Long reads or contigs
- Examples with Test data
Getting started? Check our Workflows page for step-by-step instructions on:
- How to use raw paired-end reads
- How to use cleaned/trimmed reads
- How to use long reads or assembled contigs
For quick answers to common questions, see our FAQ.
Database Setup & Configuration
Troubleshooting & Error Messages
System Requirements & Performance
If you encounter a problem that isn't answered in the FAQ, please report an issue so we can help and improve our documentation.
The Eukfinder paper has been published in mBio as of April, 2025: Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.
As of April 2025, we are providing pre-built Eukfinder databases for users to download.
For all available downloads, please refer to Eukfinder Databases.
Dayana E. Salas-Leiva
Dandan Zhao
Katherine A. Dunn
Jason Shao
For technical issues, bug reports, and code contributions, please submit a github issue
Page Updated: 2025/04/22