DuctApe
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Features A flexible software suite

Easy genomics
Many options to map proteins to the KEGG database; easy and accurate pangenome reconstruction
Painless phenomics
Easy import of phenomic data; fast growth parameters extraction; curves categorization and comparisons
Metabolic insights
Genomics and phenomics data are compared in KEGG metabolic maps
Portable
All the analysis are saved in a single file, to avoid complexity and to encourage exchange of data
Powerful
Many analyses are parallelized for an efficient use of multi-core computers

Experimental setups The three flavours of DuctApe

  • Single

    Simple genomics and phenomics analyses on a single strain.

  • Mutants

    One or more mutants of a reference strain can be added, (deletion and insertion). The mutants genome and phenome will be compared to the reference strain.

  • Pangenome

    Multiple strains can be added simultaneously. The pangenome can be calculated using the BBH algorithm and the pangenome is used in the metabolic network reconstruction.

Flexible tools The three modules of DuctApe

  • dgenome

    • Maps the proteins to the KEGG database
    • Constructs the pangenome
    • Outputs stats about the input genomes

  • dape

    • Project setup
    • Metabolic network reconstruction
    • Imports/exports KEGG data

  • dphenome

    • Imports the Phenotype Microarray experiments
    • Extracts the growth parameters and calculates the Activity Index
    • Creates growth curves plots
    • Checks the replica consistency
    • Maps the Phenotype Microarray compounds to the KEGG database
    • Outputs stats about the input phenome