dadaist2-exporter

dadaist2-exporter - tool to export dadaist2 output into MicrobiomeAnalyst compatible format. MicrobiomeAnalyst can be used as an R module or via the user-friendly website https://www.microbiomeanalyst.ca/ and Rhea (https://lagkouvardos.github.io/Rhea/).

Author

Andrea Telatin andrea.telatin@quadram.ac.uk

Synopsis

dadaist2-exporter [options] -i INPUT_DIR

Parameters

  • -i, –input-directory DIRECTORY

    Directory containing the paired end files in FASTQ format, gzipped or not.

  • -o, –output-directory DIRECTORY

    Output directory, by default will be a subdirectory called MicrobiomeAnalyst inside the input directory.

  • –skip-rhea

    Do not create the Rhea subdirectory and its files.

  • –skip-ma

    Do not create the MicrobiomeAnalyst subdirectory and its files.

  • –version

    Print version and exit.

Output

The output directory will contain:

  • metadata.csv

    Metadata file to be used in the omonymous field.

  • table.csv

    Feature table to be used in the ‘OTU/ASV table' field.

  • taxonomy.csv

    Taxonomy table to be used in the ‘Taxonomy table' field.

  • seqs.fa

    Not used in MicrobiomeAnalyst, but kept for reference.

Source code and documentation

The program is freely available at https://quadram-institute-bioscience.github.io/dadaist2 released under the MIT licence. The website contains further DOCUMENTATION.