Empty sequences cause problems with downstream tools including submission of demultiplexed, trimmed reads to ENA.
If you do not use this option, reads that have a length of zero (empty reads) are kept in the output. Some downstream tools may have problems with zero-length sequences. In that case, specify at least -m 1.
See Cutadapt documentation. Should use
-m/--minimum-lengthoption.Empty sequences cause problems with downstream tools including submission of demultiplexed, trimmed reads to ENA.