LotuS: an efficient and user-friendly OTU processing pipeline. gut metagenome

Here we present LotuS (less operational taxonomic units scripts), a fast and user-friendly open-source tool to calculate denoised, chimera checked, operational taxonomic units (OTUs). These are the basis to generate taxonomic abundance tables and phylogenetic trees from multiplexed, next-generation sequencing data (454, illumina MiSeq and HiSeq). LotuS is outstanding in its execution speed, as it can process 16S rDNA data up to two orders of magnitude faster than other existing pipelines. This is partly due to an included stand-alone fast simultaneous demultiplexer and quality filter C++ program, sdm (simple demultiplexer), which comes packaged with LotuS. Additionally, we sequenced two miSeq runs with the intent to validate future pipelines by sequencing 40 technical replicates; these are made available in this work. We show that LotuS analyses microbial 16S data with comparable or even better results than existing pipelines, requiring a fraction of the execution time and providing state of the art denoising and phylogenetic reconstruction.