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KEGGDecoder

GitHub repository: speeding-up-science-workshops/KEGGDecoder-heatmap/

DOI: 10.5281/zenodo.3519348

Binder

Summary

  • Designed to parse and visualize a KEGG-Koala output to determine the completeness of biogeochemically-relevant metabolic pathways
    • metabolic pathways are hand-curated to select for informative markers of predicted function
  • The immediate input for KEGGDecoder is a tab-delimited KEGG-Koala output file that consists of a formatted gene ID and a correspoding KEGG Ontology assignment
    • Options for generating a KEGG-Koala output include:
    • KEGG Ontology assignment requires a protein fasta file for submission and can be generated by tools such as:
      • Prodigal
      • MetaSanity - which can generate both a protein FASTA file and a KEGG-Koala output for a set of genomes

Authors

  • Author Name, github id (and ORCID if you have it)
  • Benjamin Tully, bjtully, 0000-0002-9384-7635
  • Taylor Reiter, taylorreiter, 0000-0002-7388-421X
  • Luiz Irber, luizirber, 0000-0003-4371-9659
  • Roth Conrad, rotheconrad, 0000-0001-8155-8441
  • Jay Osvatic, osvatic, 0000-0002-7765-0058
  • Chris Neely, cjnelly10, 0000-0002-2620-8948
  • Marisa Lim,
  • Jason Fell, jfell13, 0000-0001-6680-2936