Quick Start Examples

Genome examples

• All databases

conda activate metacerberus
metacerberus.py --prodigal lambda.fna --hmm ALL --dir_out lambda_dir

• Only KEGG/FOAM all

conda activate metacerberus
metacerberus.py --prodigal lambda.fna --hmm KOFam_all --dir_out lambda_ko-only_dir

• Only KEGG/FOAM prokaryotic centric

conda activate metacerberus
metacerberus.py --prodigal ecoli.fna --hmm KOFam_prokaryote --dir_out ecoli_ko-only_dir

• Only KEGG/FOAM eukaryotic centric

conda activate metacerberus
metacerberus.py --fraggenescan human.fna --hmm KOFam_eukaryote --dir_out human_ko-only_dir

• Only Viral/Phage databases

conda activate metacerberus
metacerberus.py --prodigal lambda.fna --hmm VOG, PHROG --dir_out lambda_vir-only_dir

Tip

You can pick any single database you want for your analysis including KOFam_all, COG, VOG, PHROG, CAZy or specific KO databases for eukaryotes and prokaryotes (KOFam_eukaryote or KOFam_prokaryote).

• Custom HMM

conda activate metacerberus
metacerberus.py --prodigal lambda.fna --hmm Custom.hmm --dir_out lambda_vir-only_dir

Illumina data

• Bacterial, Archaea and Bacteriophage metagenomes/metatranscriptomes

conda activate metacerberus
metacerberus.py --prodigal [input_folder] --illumina --meta --dir_out [out_folder] 

• Eukaryotes and Viruses metagenomes/metatranscriptomes

conda activate metacerberus
metacerberus.py --fraggenescan [input_folder] --illumina --meta --dir_out [out_folder] 

Nanopore data

• Bacterial, Archaea and Bacteriophage metagenomes/metatranscriptomes

conda activate metacerberus
metacerberus.py --prodigal [input_folder]  --nanopore --meta --dir_out [out_folder]

• Eukaryotes and Viruses metagenomes/metatranscriptomes

conda activate metacerberus
metacerberus.py --fraggenescan [input_folder] --nanopore --meta --dir_out [out_folder] 

PacBio data

• Microbial, Archaea and Bacteriophage metagenomes/metatranscriptomes

conda activate metacerberus
metacerberus.py --prodigal [input_folder]  --pacbio --meta --dir_out [out_folder]

• Eukaryotes and Viruses metagenomes/metatranscriptomes

conda activate metacerberus
metacerberus.py --fraggenescan [input_folder]  --pacbio --meta --dir_out [out_folder]

SUPER (both methods)

conda activate metacerberus
metacerberus.py --super [input_folder]  --pacbio/--nanopore/--illumina --meta --dir_out [out_folder]

Important

Fraggenescan will work for prokaryotes and viruses/bacteriophage but prodigal will not work well for eukaryotes.