The fastx_mask command performs
low-complexity masking of sequences in a FASTA or FASTQ file.
option specifies the
masking algorithm to use. Default is fastnucleo or fastamino.
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.
usearch -fastx_mask reads.fastq -fastqout masked.fastq -qmask
dust -min_unmasked_pct 50