cgeb2001's DokuWiki!

You've loaded an old revision of the document! If you save it, you will create a new version with this data.

====== 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
-----------------------------------------------------------

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.

3. Eukfinder v1.2.4 is not yet installed globally on Perun.

//How to Run Eukfinder v1.2.4 on Perun//

source activate eukfinder
   Eukfinder=/misc/scratch3/Eukfinder/eukfinder.py
   python $Eukfinder [arguments]

Please fill all the letters into the box to prove you're human. J W H J K Please keep this field empty:

Edit summary

Note: By editing this page you agree to license your content under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International