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--- decontamination_using_read_classifier_a.k.a_eukfinder [2019/09/09 08:02] – created 24.138.68.92
+++ decontamination_using_read_classifier_a.k.a_eukfinder [2026/01/21 12:34] (current) – 172.20.46.175
@@ Line 1: / Line 1: @@
-I will be posting the protocol here as well as the instructions.
+====== Decontamination using Eukfinder ======
-Cheers, D
+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//
+. The newest version removes the need for acc2tax.
+. Only Centrifuge_DB and PLAST_DB are required.
+<Last updated by Jason Shao on Jan 21, 2026>