title: From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.
abstract: The development of high-throughput sequencing technologies has provided microbial ecologists with an efficient approach to assess bacterial diversity at an unseen depth, particularly with the recent advances in the Illumina MiSeq sequencing platform. However, analyzing such high-throughput data is posing important computational challenges, requiring specialized bioinformatics solutions at different stages during the processing pipeline, such as assembly of paired-end reads, chimera removal, correction of sequencing errors, and clustering of those sequences into Operational Taxonomic Units (OTUs). Individual algorithms grappling with each of those challenges have been combined into various bioinformatics pipelines, such as mothur, QIIME, LotuS, and USEARCH. Using a set of well-described bacterial mock communities, state-of-the-art pipelines for Illumina MiSeq amplicon sequencing data are benchmarked at the level of the amount of sequences retained, computational cost, error rate, and quality of the OTUs. In addition, a new pipeline called OCToPUS is introduced, which is making an optimal combination of different algorithms. Huge variability is observed between the different pipelines in respect to the monitored performance parameters, where in general the amount of retained reads is found to be inversely proportional to the quality of the reads. By contrast, OCToPUS achieves the lowest error rate, minimum number of spurious OTUs, and the closest correspondence to the existing community, while retaining the uppermost amount of reads when compared to other pipelines. The newly introduced pipeline translates Illumina MiSeq amplicon sequencing data into high-quality and reliable OTUs, with improved performance and accuracy compared to the currently existing pipelines.
authors.affiliation: Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium.|Department of Bio-Engineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium.|VIB Center for the Biology of Disease, VIB, Herestraat 49 - box 1028, 3000 Leuven, Belgium.|Department of Microbiology and Immunology, REGA institute, Herestraat 49 - box 1028, 3000 Leuven, Belgium.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Mysara
authors.affiliation: Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium.
authors.forename: Mercy
authors.initials: M
authors.lastname: Njima
authors.affiliation: Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium.
authors.forename: Natalie
authors.initials: N
authors.lastname: Leys
authors.affiliation: Department of Bio-Engineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussel, Belgium.|VIB Center for the Biology of Disease, VIB, Herestraat 49 - box 1028, 3000 Leuven, Belgium.|Department of Microbiology and Immunology, REGA institute, Herestraat 49 - box 1028, 3000 Leuven, Belgium.
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.affiliation: Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400 Mol, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Monsieurs
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D058893:DNA Barcoding, Taxonomic; D030561:Databases, Nucleic Acid; D056186:Metagenomics / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D064878:Web Browser
keywords: 16S rRNA metagenomics; OTU clustering; amplicon sequencing; chimera; denoising; operational taxonomic units