Question: fqtrim minimum read length default value
This means any reads that gets shortened less than 16bp will be removed. Its clearly stated in manual.
minimum read length after trimming; if the read sequence is shorter than this, before or after the requested trimming filters, the read is discarded (trashed). Default: 16.
In other words, the shorted read will be 16bp after the trimming. All reads less than 16bp will be discarded.