LotuS2

LotuS2 is an ultrafast and highly accurate tool for amplicon sequencing analysis.

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

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand