EukCC

Coverage.py coverage

EukCC is a completeness and contamination estimator for metagenomic assembled microbial eukaryotic genomes.

Documentation

Head over to https://eukcc.readthedocs.io/ to check out the documentation.

Run

Download EukCC2 database from FTP

# 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_1.2.tar.gz
tar -xzvf eukcc2_db_ver_1.2.tar.gz
export EUKCC2_DB=$(realpath eukcc2_db_ver_1.2)

Quickstart using 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

Bioconda / pip

Alternatively you can install EukCC using conda or pip.

In addition, you need to install mandatory requirements:

metaeuk=4.a0f584d
pplacer
epa-ng=0.3.8
hmmer=3.3
minimap2
bwa
samtools

Outputs explanation

eukcc.log - log of execution

eukcc single

eukcc.csv - table with estimated completeness, contamination and taxonomy lineage

eukcc folder

eukcc.csv - table with estimated completeness, contamination and taxonomy lineage for good quality bins
merged_bins.csv - table of merged refined bins
bad_quality.csv- table with estimated completeness, contamination and taxonomy lineage for bad quality bins (chosen marker gene set is supported by less than half of the alignments)
missing_marker_genes.txt - line separated list of bins with not defined set of marker genes
merged_bins - folder with merged bins sequences
refine_workdir - working directory with intermediate steps results

Don’t use EukCC on already pubished data

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.

Cite

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.

Changed compared to EukCC 1

Note: With version 2, EukCC should provide a better experience than version 1. Version 2 is not compatible with previous versions, most commandline arguments changed. So version 2 is not a drop in replacement.

Users can set the prevalence threshold for marker sets. In EukCC 1 this was fixed to 98% single copy prevalence. Now users could change that to be more strict. We find that often 100% single copy prevalence can be found.

Issues and bugs

Please report any bugs and issues here on GitHub. Make sure to include the debug log (run eukcc using --debug flag).

used exit codes

200: File not found
201: No Marker gene set could be defined
202: No database provided
203: Corrupted file
204: Predicted zero proteins
222: Invalid settings