A bioinformatics tool designed to enable rapid recovery of high-quality draft genomes of microbial eukaryotes from various environmental metagenomic samples.
Github: https://github.com/RogerLab/Eukfinder
Use Guide (work in process): https://github.com/RogerLab/Eukfinder/wiki
Conda installation package: https://anaconda.org/bioconda/eukfinder
Binning Workflow (work in process): https://github.com/RogerLab/MetagenomeBinningWorkflow
Tips and Tricks Talk Slides: https://perun.biochem.dal.ca/downloads/icgvideo/TAT/TT_Apr24_Eukfinder_Anvio.pdf
Warning! Eukfinder is not deadlock-safe, please avoid running parallel instances!
Updated Database Locations for Eukfinder (v1.2.4)
Centrifuge: /scratch3/Eukfinder/DB/Centrifuge_DB/ (Sept 2020, gut environment focused)
/scratch3/Eukfinder/DB/Centrifuge_DB_2024/ (Nov 2024, marine environment focused)
/scratch5/db/Eukfinder/Centrifuge/ABV/ (Apr 2025, Bacteria/Archaea/Virus refseq)
PLAST: /scratch3/Eukfinder/DB/PLAST_DB/ (Sept 2020, gut environment focused)
/misc/scratch3/Eukfinder/DB/PLAST_DB_2024/ (Nov 2024, marine environment focused)
Important Notes for v1.2.4
1. The newest version removes the need for acc2tax.
2. Only Centrifuge_DB and PLAST_DB are required.
<Last updated by Jason Shao on Jan 21, 2026>