Illumina reads to be processed and prepared for reference genome alignment

Question

[Veselina]

Hello to all! I have to align sequence reads obtained by Illumina HiSeq/Nova to a reference genome. The sequencing was carried out using 2x150 paired-end configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 on the HiSeq instrument. I will use the Galaxy web-tool (BWA-MEM2) for the alignment. However, the reads have not been processed and probably need trimming. I attached below the FastQC - per base sequence quality images. Could you please suggest how I can do that? Thank you!

1Reverse reads_per base sequence quality[Forward reads_per base sequence quality]

[Michael]

I'd just process them with fastp (should be in Galaxy too). The tool will determine by itself whether trimming is necessary.

[shelkmike]

I concur. In most cases I just use Fastp with default parameters.