eukcc 0.0.1

Check eukaryotic genomes or MAGs for completeness and contamination

EukCC

Estimate completeness and contamination in Eukaryotes.

this software is under development and unstable. Updates might break or enhance your experience

Install

Dependencies

GeneMark-ES

If you want to predict genes install GeneMark-ES: http://exon.gatech.edu/GeneMark/license_download.cgi

For this you need some perl libraries installed:

cpan install YAML
cpan install Logger::Simple
cpan install Parallel::ForkManager.pm

HMMER

Just install HMMER from: http://hmmer.org/

I used version 3.2.1 but any later version should work fine.

Pplacer

Install pplacer. I installed it via conda:

conda install -c bioconda pplacer 

I used version 1.1alpha19

The package

Get the database:

git clone https://gitlab.ebi.ac.uk/saary/eukcc
cd eukcc
python3 setup.py sdist bdist_wheel
pip3 install dist/eukcc-0.0.1.tar.gz

Run it

EukCC.py --help

Example

Run EukCC on a bunch of bins:

EukCC.py -c config/dir outdir bins/*.fa

FAQ

GeneMark-ES throws a lot of errors Yes, id does. If it does not start at all try the 32 bit version (with the 32 bit version licence). This worked for me.