I have been using the generic pipeline suggested in the Tutorials sections, 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
- Adapter and Quality Trimming all four files per sample
- Concatenate all four files into a single file
- Run diamond on this single file
- 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?