The pipeline currently returns an unfiltered fasta file with all (taxonomy annotated) sequences. If a primer file is provided it additionally returns a file with the filtered/cropped/oriented sequences. However, preliminary tests revealed that many sequences get lost in this step so it might be good to create a combined output file with filtered sequences if available and raw sequences for all the others.
The pipeline currently returns an unfiltered fasta file with all (taxonomy annotated) sequences. If a primer file is provided it additionally returns a file with the filtered/cropped/oriented sequences. However, preliminary tests revealed that many sequences get lost in this step so it might be good to create a combined output file with filtered sequences if available and raw sequences for all the others.