I'm trying to filter out any reads that consist of more than 50% low quality reads (Q<20). I've already performed filtering steps to remove adapter contamination and remove reads with more than 10% unknown reads, both using cutadapt. Can anyone recommend a tool to use to perform this filtering step? I've previously seen NGSQC Toolkit recommended but I believe this is not supported any longer and I am having trouble accessing it.
Also I am using paired end reads so do these need to be processed together and do I need to use a tool that supports this?