I have reads generated for metagenome sequence using Illumina Miseq paired-end reads with the read length of 250 bp. I want to perform the quality check for the obtained sequence.
Could anyone please let me know the software that can be used? I read about Prinseq standalone version but it has various options. I am a little confused about which parameters to use.
I want to remove sequences that have Phred score below 20.