I’m new to bioinformatics and metagenomic analysis and I have been asked to analyse paired end metagenomic sequences using diamond and MEGAN. Does anyone know the best way to go about this. I was thinking to align the reads to the NCBI database seperately using diamond, giving me two outputs per sample. Then I could select paired reads when importing from BLAST and select both diamond outputs for the sample. This should give me one MEGAN file I can then use to compare to the other samples after they have all been merged and meganised right? Do I need to meganise the samples all separately or is there a faster way via bash commands that allow the specification of paired reads?
Does anyone have any experience or advice? I have over 150GB of data to analyse and I’m worried I should be doing a number of steps before using diamond, I’m just not sure what they would be.
Thanks in advance.