One of the steps in the 16sRNA pipeline is concatinating/pooling reads from different samples (in order to study the beta diversity).
For example I can use the cat command as following
cat sample1_R1.fastq sample2_R1.fastq sample3_R1.fastq >> tot.fastq
and go ahead and remove chimera, label OTUs and etc. However, I wonder how can I look back and figure out which sample has came from what subject ?! Of course I can make a script to look up reads and assing them to subject; but I thought there might already be something exists