I have some metagenomic shotgun sequencing data that is paired-end. I am considering using metaphlan2 and the biobakery workflows for analysis. However, the documentation states that they recommend merging the paired-end sequencing data into one before beginning the analysis. My question is:
1.) Should I merge the sequencing data and the trim them? 2.) Should I trim and then merge? 3.) How do I merge the datasets?