I need to map a bunch of fastq files consisting of DNA sequences (paired end reads) against pan-genome proteins. So I need to align DNA sequences against proteins sequences. I used DIAMOND (which was very fast and user friendy), however later on I figured out it does not support paired-end reads. So I am looking for another tool to do it. I thought BlastX could do the job for me, but I am not sure if it can handle paired end reads or not?
I would appreciate if anyone who has experience with Blast let me know if using BlastX is an appropriate way for this purpose or if there is any other tool that I can use. Thanks