Less OTU scripts and sdm, a simple demultiplexer

LotuS2 is a complete amplicon pipeline and quality filter


LotuS2 is a lightweight complete 16S/18S/ITS pipeline to:

  • demultiplex and filter fasta or fastq sequences
  • denoise, remove chimeric sequences and cluster sequences into very high quality OTUs/ASVs that perform at a similar level to mothur / dada2
  • remove background contamination (e.g. host dna)
  • determine taxonomic origin of each OTU using >5 specialized and general purpose database or statistical algorithms
  • construct OTU, genus, family, class, order and phylum abundance tables in .txt or .biom format
  • reconstruct OTU phylogenetic tree
  • generate phyloseq objects for downstream analysis



  • is the fastest pipeline currently available
  • allows for analyzing hiSeq amplicon data on a laptop
  • output is easily integrateable into existing workflows such as R, QIIME2/mothur or Matlab
  • comes with sdm which is a powerful and blazingly fast demultiplexer and read filter


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