EukCC options explained

EukCC in genome (default) mode

When launching EukCC without special parameters, it will assume that a genomic fasta file was passed as input. Thus GeneMark-ES will be used to predict proteins.

eukcc --db eukccdb -o . genome.fna

EukCC in protein mode

If proteins for a genome or MAG were already predicted using a nother pipeline, EukCC can be used to estimate the completeness and contamination.

For this EukCC requires at least the proteins as Fasta file. Internally EukCC ignores repeated proteins that occure very close to each other on a genomic level. This is due to common gene prediction errors and subsequent duplicated hits with profile hmms. Thus it is possible to pass the genomic coordinates for each protein as a bed file to EukCC. Such a file can easily be prepared from gtf or gff files. If no bed file is provided, this step will be skipped.

The bed file needs to be a simple five column bed file containing the contig, start and end of the gene, the strand and finally the name of the gene. Exons and introns are ignored as only start and end of the coding regions matter.

Befor submitting predicted proteins make sure to remove any stop codons (*), as they cause issues with pplacer (https://github.com/Finn-Lab/EukCC/issues/14).

eukcc --db eukccdb -o . \
      --protein genome.faa \
      --bed coordinates.bed

EukCC using pygmes

GeneMark-ES uses a self training step to generate a model for the provided genome. Somtimes highly fragmented or incomplete genomes can fail to provided enough training data for GeneMark-ES model creation to succeed.

In these cases EukCC can rely on pygmes to select a suitable model from previous analysed genomes. This allows to estimate genome completeness also for very incomplete genomes.

For pygmes to select a suitable model the user needs to provide a diamond data base with taxonomic information. Such a database can be downloaded here:

wget -O uniref50_pygmes.dmnd http://ftp.ebi.ac.uk/pub/databases/metagenomics/eukcc/uniref50_20200213_tax.dmnd

EukCC can then be launched with:

eukcc --db eukccdb -o . \
    --pygmes \
    --diamond uniref50_pygmes.dmnd \
    genome.fna

EukCC -h