Flexible and fast amplicon sequencing analysis

SSU, LSU, ITS, Qualify filtering, 6 clustering options, OTUs + ASVs and much more in one pipeline.

Paper now available!



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)
  • remove background contamination (e.g. host dna)
  • determine taxonomic origin of each OTU using >5 specialized and general purpose database or statistical algorithms that achieve the highest fraction of species level assigments among all platforms
  • 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


  • LotuS2 is the fastest contemporary amplicon sequencing pipeline
  • It allows for analyzing hiSeq amplicon data on a laptop
  • The output is easily integrateable into existing workflows such as R, QIIME2/mothur or Matlab
  • Further, it comes with sdm which is a powerful and ultrafast demultiplexer and read filter


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