title: LotuS: an efficient and user-friendly OTU processing pipeline.
abstract: 16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools.
  
  
  
  Here we present the less operational taxonomic units scripts (LotuS), 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, simple demultiplexer (sdm), 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. LotuS is available through the following URL: http://psbweb05.psb.ugent.be/lotus .
authors.affiliation: Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium.|Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium.|Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Hildebrand
authors.affiliation: Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium.|Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium.|Department of Microbiology and Immunology, REGA institute, KU Leuven, Herestraat 49, Leuven, 3000, Belgium.|VIB Center for the Biology of Disease, Herestraat 49, Leuven, 3000, Belgium.
authors.forename: Raul
authors.initials: R
authors.lastname: Tadeo
authors.affiliation: Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany.|Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
authors.forename: Anita Yvonne
authors.initials: AY
authors.lastname: Voigt
authors.affiliation: Structural & Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, 69117, Germany.|Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Str, 10, Berlin, 13125, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium. jeroen.raes@med.kuleuven.be.|Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium. jeroen.raes@med.kuleuven.be.|Department of Microbiology and Immunology, REGA institute, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. jeroen.raes@med.kuleuven.be.|VIB Center for the Biology of Disease, Herestraat 49, Leuven, 3000, Belgium. jeroen.raes@med.kuleuven.be.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D004275:DNA, Ribosomal; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017421:Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: 16S rDNA gene; Demultiplexing; Metagenomics; OTU; Pipeline