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Output files - results

MAGset returns two types of final results: HTML pages and CSV files.

HTML pages

The generated html pages are available in {output_folder}/result/html:

  • Index with ANI results, pangenome summary (*), genomic regions of interest summary, annotations summary (*), MAGcheck summary
  • Advanced gene search (*)
  • Pangenome charts (*)
  • Pangenome genes list (*)
  • Genomic regions of interest
  • Annotations (*)

*These data/pages are available just if the input are Genbank files.

CSV files

The html result has more information/details, but some results are also in CSV format. The CSV files are available in {output_folder}/result/csv:

  • summary.csv, with the columns:
    • genome_name
    • pangenome_genes_qty (*)
    • pangenome_specific_genes (*)
    • pangenome_shared_genes (*)
    • pangenome_core_genes (*)
    • pangenome_discarted_genes (*)
    • gris
    • genes_in_gris (*)
    • gris_found_by_magcheck
    • genes_in_gris_found_by_magcheck (*)
    • cog_annotations (*)
    • cazy_annotations (*)
  • gri_list.csv, with the list of found gris

*These data are available just if the input are Genbank files.

More result files

All intermediated files are available in {output_folder}. If you need the .fasta sequence files of the GRIs (genomic region of interest), they can be found in {output_folder}/03_gris/clustered/.