I have a pair of RNA fastq files that are heavily contaminated with rRNA sequences, to such extent that almost one half of reads originate from a 10K long sequence of reference. I want to remove these reads, and I know I can do it at BAM level in one of many ways (ike Samtools View), but I am curious if there is an efficient way of removing those reads at the fastq stage. The idea is to speed up the alignment in some way.
Is that a good way to remove unwanted reads prior to alignment, in order to speed up the processing? Maybe a trimming tool, or such?