It is a CSV file with a the number of columns that depends on the number of sequences/samples that are processed in the PEMA run. The first column is an ID. The final column contains the species information. The columns in between are for each sequence (each sample) that was processed and contain integers values; the title of these columns is the ENA code of the sequence (the same as in the MasterARMS csv file).

The output from PEMA is organised into a directory structure that depends on the details in the Parameter.tsv file (e.g. which sequence type was processed, what algorithm was chosen, etc.).

This is an input parameter file used for running PEMA on COI marker gene data in the ARMS Internal Joint Initiative workflow. It is a tsv file that can be uploaded in order to specify which sequence (which column gene_18S, gene_COI, gene_ITS) is chosen. It is a well-defined template and the user is required to modify certain fields only.