There is a Perl and Python version which esentially do the same.

Perl script that masks bases as "N"s given a PHRED quality threshold.

The program is loosely based on SubN published by Yun and Yun (2014). The main difference is that mask_fastq.pl can natively handle I/O compressed (gzipped) files and does not depend on any external modules.

git clone https://github.com/santiagosnchez/mask_fastq
cd mask_fastq
chmod +x mask_fastq.pl
sudo cp mask_fastq.pl /usr/local/bin

Use the -h flag for more details:

perl mask_fastq.pl -h

#########################
# Running mask_fastq.pl #
#########################

Try:

perl mask_fastq.pl -f myseqs.fastq(.gz) [ -q PHRED_VALUE ]

wget https://raw.githubusercontent.com/santiagosnchez/mask_fastq/master/mask_fastq.py

python mask_fastq.py my_fastq_file.fq.gz 55

The number at the end is the Phred quality score limit. By default it will be 50 (e.g. if not provided).

Yun, Sajung, & Yun, S. (2014). Masking as an effective quality control method for next-generation sequencing data analysis. BMC Bioinformatics, 15(1), 152–8. http://doi.org/10.1186/s12859-014-0382-2