LotuS2 (less OTU scripts) is a lightweight complete 16S/18S/23S/28S/ITS pipeline that is able to ..
demultiplex and filter fasta or fastq sequences
denoise, remove chimeric sequences and cluster sequences into very high quality OTUs/ASVs that performs better than mothur / dada2 (Preprint Figure 3, Preprint Figure 4)