The input must contain a genome file or DNA and Protein gene file or just Protein gene file.


  1. Input is a genome sequence (input.fasta).
gmgc-mapper -i input.fasta -o output

GMGC-mapper will call prodigal to predict genes and then process each gene.

  1. Input is DNA/protein gene sequences (genes.fna and genes.faa, respectfully).
gmgc-mapper --nt-genes genes.fna --aa-genes genes.faa -o output
gmgc-mapper --aa-genes genes.faa -o output

Processing metagenomes using NGLess

If your input is metagenome, you can use NGLess for assembly and gene prediction and, then, pass the results to GMGC-mapper.


The recommended way to install NGLess is through bioconda:

conda install -c bioconda ngless 

Assembly and gene prediction

ngless "1.0"

sample = 'SAMEA2621155'
input = load_mocat_sample(sample)

preprocess(input, keep_singles=False) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:

contigs = assemble(input)
write(contigs, ofile='contigs.fna')

orfs = orf_find(contigs)
write(contigs, ofile='orfs.fna')