Pavian

In MobaXterm:

• Open an SFTP session
• Navigate to the directory where you ran the workflow, using the absolute path
  • eg, /isilon/lacombe-rdc/users/tranlan/cas_2020
  • Navigate to the file with a name similar to cas_kraken2
• Download the report.txt files

At the Pavian site

• On the “Data Selection” page:
  • Upload all the report.txt files
    • NB: the Pavian site times out after relatively short amount of time if left inactive, and when it does you have to re-upload the desired files
    • At the moment there have been some problems encountered when trying to run Pavian on R, but in theory it should be possible

      Retrieving specific taxa level tables:

• To access the resources needed to generated the NMDS and bar graphs, go to the “Comparison” page:
  • Change the rank preference from “Any Rank” to “Species”
  • Change “Reads” to “%”
    • Make sure you unselect “Reads”, rather than just add percentages to the number of reads
  • Remove Apis mellifera and Varroa reads from the data by selecting their respective rows and then clicking the golf tee symbol at the top of the page
  • Download a .tsv version of this data using the button at the bottom of the page

Retrieving 1 table with all taxa levels:

• Go to the "Comparison" page
• Make sure Collapse taxa with no reads is NOT selected
• Choose Reads OR % (not both)
• Filter out taxa at your discretion
• Download a .tsv version of this data using the button at the bottom of the page

If you wish to see a Sankey visualization of all species present in each sample, go to the “Sample” page

• NB: viruses, in particular the phiX bacteriophage, have been filtered out by the snakemake workflow. The BeeRoLaMa database does not contain virus sequences.