I have several fastq.gz files from multiple WGS sequencing runs that I would like to merge. Can I do this in the same way that you would merge any other read files? For example, my files look something like the following:
hey!
If you import them using the manifest method (really easy) to a .qza then they become a single artifact you can use on qiime2 =D if you need it for something that requires fastq.gz format then just export it to one big ole fastq (sorry theres not a one step method i can think of off the top of my head
So the issue is that you have replicates for each sample and you want these merged together?
As @mouldinator mentioned, importing fastq data into QIIME 2 using the manifest format of casava 1.8 format will cause these to be imported into a single artifact. Downstream analysis should be streamlined so you do not need to worry about juggling multiple files, and merging multiple runs will happen further downstream.
Otherwise, QIIME 2 is probably not the tool for the job, e.g., if you want to merge before inputting to a different program. In that case, you should probably just use some basic bash commands to gzunip, cat, and gzip based on filename and read direction.