EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.
With version 2, EukCC should provide a better experience than version 1. We aim at creating a stable package with long term support.
Note: Version 2 is not compatible with previous versions, most commandline arguments changed. So version 2 is not a drop in replacement.
Head over to https://eukcc.readthedocs.io/ to check out the documentation.
Here a super fast overview on how to get started using singularity. For more information please see the documentation.
# create a folder were to keep the database
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
export EUKCC2_DB=$(realpath eukcc2_db_ver_1.1)
# fetch and launch container
singularity pull docker://quay.io/microbiome-informatics/eukcc
singularity exec eukcc_latest.sif eukcc single -h
Alternatively you can install EukCC using pip, but we recommend using the container.
Get EukCC quickly by fetching the container.
The container is hosted and automatically build from the master branch here: https://quay.io/repository/microbiome-informatics/eukcc
docker pull quay.io/microbiome-informatics/eukcc
singularity pull docker://quay.io/microbiome-informatics/eukcc
If you installed version 2: make sure to also fetch the database for version 2:
http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/
Or at least not without thinking about it:
You should not use EukCC on already published genomes, if they have used during training of the marker
gene sets. If you want to make sure, you can see all used accessions in the database file db_base/backbone/base_taxinfo.csv
.
If you use EukCC make sure to cite:
Saary, Paul, Alex L. Mitchell, and Robert D. Finn.
"Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC."
Genome biology 21.1 (2020): 1-21.
EukCC also uses metaEUK, hmmer, pplacer, ete3 and epa-ng.
Please report any bugs and issues here on GitHub. Make sure to
include the debug log (run eukcc using --debug
flag).