Truncates sequences in a FASTA or FASTQ file at a fixed length given by the -trunclen option. Shorter sequences are discarded.
Output is written to -fastaout (FASTA) and/or -fastqout (FASTQ). You cannot use -fastqout if the input is FASTA because the quality scores are not known.
The -stripleft n option removes n letters at the start of a sequence. (Requires v8.0.1611 or later).
The -stripright n option removes n letters at the end of a sequence. (Requires v8.0.1611 or later).
The -padlen n option appends Ns at the end of the sequence as needed to increase the length to n. If the length is already >= n, then the sequence is unchanged. (Requires v8.0.1611 or later).
The -label_suffix option specifies a string that is appended to the labels in the output file(s).
Example
usearch -fastx_truncate reads.fastq -trunclen 200 -label_suffix
_200 -fastaout reads_200.fa