ı have a campylobacter WGS raw data (paired fastq). How do I upload this raw data (FASTQ) to MEGAN? I did not see the fastq option in the options section.
You first have to use the DIAMOND alignment program to align your reads against the NCBI-nr database so as to produce a DAA file. This DAA file is then meganized and then can be opened in MEGAN. Please se the MEGAN paper for details: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004957