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manuscript_data_availability.md

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Availability of the data used in the publication:

  • Nimagen and synthetic ARTIC amplicon sequences are available at the European Nucleotide Archive, BioProject accession PRJEB53222.
  • Real wastewater samples used for parameter estimation, sequenced using the ARTIC v3 protocol are available on request and with permission from the Joint Biosecurity Centre and University of Liverpool.
  • Summarised data (e.g. amplicon counts) are available through GitHub at https://github.com/goldman-gp-ebi/SWAMPy/tree/main/supplementary_files.
  • The samples used for validation and comparison with ww_simulations are available at ENA BioProject accession PRJNA796340, with the exact samples used listed in the supplementary information file.
  • Non-default SWAMPy options used to generate the 73 simulated time point data used in the manuscript:
-ins 0.0002
-del 0.00115
-subs 0.005
-rins 0.0002
-rdel 0.00115
-subs 0.005
--amplicon distribution dirichlet 2
--amplicon pseudocounts 200