From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data

Mohamed Mysara, Mercy Njima, Natalie Leys, Jeroen Raes, Pieter Monsieurs

Research output: Contribution to journalA1: Web of Science-article

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.

Original languageEnglish
JournalGigaScience
Volume6
Issue number2
Pages (from-to)1-10
Number of pages10
ISSN2047-217X
DOIs
Publication statusPublished - 1-Feb-2017
Externally publishedYes

Keywords

  • Algorithms
  • Computational Biology/methods
  • DNA Barcoding, Taxonomic
  • Databases, Nucleic Acid
  • Metagenomics/methods
  • Sequence Analysis, DNA/methods
  • Software
  • Web Browser

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