I have been using a generic pipeline for processing a recent metagenomics dataset that I received.
Samples were sequenced on two lanes on the HiSeq. Thus, I have 4 sets of reads per sample i.e. Reads 1 and 2 from Lane 1 and Reads 1 and 2 from lane 2
My workflow has been the following 1. Adapter and Quality Trimming all four files per sample 2. Concatenate all four files into a single file 3. Run diamond on this single file 4. Then use Megan6 for further processing
Can anyone please advise if Step 2 is appropriate in my case or is it better to process each lane separately?