Quickstart

Setup

EukCC is avaliable to install frommany soruces. We reccomend using our Docker container:

docker pull  microbiomeinformatics/eukcc

Other options are:

Bioconda (https://anaconda.org/bioconda/eukcc)

conda instal -c conda-forge -c bioconda "eukcc>=2"

pip install eukcc

You can also fetch the source code from GitHub: https://github.com/Finn-Lab/EukCC/

Database setup

You will need to fetch the database for EukCC once.

Note

The database from version 1 is not compatible. So after upadting to EukCC make sure to upadte the database.

Fetching the database is as simple as:

mkdir eukccdb
cd eukccdb
wget http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/eukcc2_db_ver_1.1.tar.gz
tar -xzvf eukcc2_db_ver_1.1.tar.gz

If you want to forget about the database location you can add an ENV variable to your .bash.rc:

export EUKCC2_DB=/path/to/.../eukcc2_db_ver_1.1

Running EukCC

EukCC comes with two modes. You can run EukCC on a single bin or on a folder of bins.

Running EukCC on a single bin gives you the most options to tweak the parameters as you see fit. For most metagenomic workflows running EukCC on a folder of bins might be the most simple thing to do.

EukCC on a single MAG

We assume that you did set you $EUKCC2_DB to the correct location. If not please use the --db flag to pass the database to EukCC.

eukcc single --out outfolder --threads 8 bin.fa

EukCC will then run on 8 threads. You can pass nucleotide fastas or proteomes to EukCC. It will automatically try to detect if it has to predict proteins or not.

By default it will never use more than a single threads for placing the genomes in the reference tree, to save memory.

EukCC on a folder of bins

eukcc folder --out outfolder --threads 8 bins

EukCC will assume that the folder contains files with the suffix .fa. If that is not the case please adjust the parameter.

In folder mode EukCC will also try to refine bins automatically. To learn more about that please see