Fastq_masker masks nucleotides with *N* (or other character) based on quality in fastq files. You will need to specify the quality threshold and select which masking letter to use (N or C)
Parent program: fastx_toolkit
FASTX-Toolkit is a software package for preprocessing output data produced by Next-Generation sequencing machines in FASTA and FASTQ format before the main processing (assembling, mapping etc.). FASTQ to FASTA conversion, statistics calculation, file customization, quality-based preprocessing, trimming and etc. can be provided.