====== Decontamination using Eukfinder ======


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>