Output is written to -fastaout (FASTA) and/or -fastqout (FASTQ). If the input file is FASTA, then you cannot use -fastqout because the base quality scores are not known.
By default, soft masking is used (lower-case). The -hardmask option can be used to specify hard masking (overwrite Ns for nucleotids, Xs for amino acids).
The min_unmasked_pct option specifies the minimum fraction of the sequence that is not masked. If a larger fraction is masked, the sequence is discarded.
The max_unmasked_pct option specifies the maximum fraction of the sequence that is not masked. If a smaller fraction is maskd, the sequence is discarded. The typical use of this option is to determine which sequences were discarded by min_unmasked_pct.
Multithreading is supported.
usearch -fastx_mask reads.fastq -fastqout masked.fastq -qmask dust -min_unmasked_pct 50