Output of GMGC-mapper

Explanation of the files in the output directory

Prodigal output

These three files are the output of prodigal (if GMGC-mapper was called in genome mode)

• prodigal_out.faa protein sequence
• prodigal_out.fna DNA sequence
• gene.coords.gbk gene information in Genebank format

Hit Table (hit_table.tsv)

The results of the queries to the GMGC.

There are five columns in the file.

• query_name: the name/id of the input gene
• unigene_id: the Unigene with the best score in the GMGC
• `align_category: there are four different classes of alignment (see below)
• gene_dna: the DNA sequence of the best hit in GMGC
• gene_protein: the protein sequence of the best hit in GMGC

Alignment category

• EXACT: at least 95% nucleotide identity with at least 95% coverage. As unigenes in the GMGC represent 95% nucleotide clusterings (species-level threshold), this would mean that the query gene would have clustered with the GMGC unigene.
• SIMILAR: at least 80% amino acid identity with at least 80% coverage.
• MATCH: at least 50% amino acid identity with at least 50% coverage.
• NO MATCH: no match in GMGC.

Genome bins (genome_bin.tsv)

Genome bins (MAGs) found in the results (and a count of how many genes are contained in them).

There are two columns in the file.

• genome_bin: the name of genome bins in GMGC
• nr_hits: the times of input genes hitting it

Note while not all GMGC unigenes are contained in a genome bin, some are contained in many. Thus, the total counts will not (except by coincidence) correspond to the number of genes queried.

Summary (summary.txt and runlog.yaml)

The file summary.txt provides a human-readable summary of the results, while runlog.yaml is a summary of run metadata (as a YaML file, it is both machine and human-readable).

The file summary.txt should be reproducible and running GMGC-mapper twice on the same input should produce the same results. By design, though, runglog.yaml includes information such as the time when the analysis was run which is not reproducible.