Usage

Commands

• -i/--input : path to the input genome file(.fasta/.gz/.bz2).

• -o/--output : Output directory (will be created if non-existent).

• --nt-genes : path to the input DNA gene file(.fasta/.gz/.bz2).

• --aa-genes : path to the input Protein gene file(.fasta/.gz/.bz2).

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

Examples

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.

Install

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:
        discard

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

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