SimpleMetaPipeline: Breaking the bioinformatics bottleneck in metabarcoding

<p style="border:0px; display:block; height:0px; left:-9999px; margin-bottom:0px; margin-left:0px; margin-right:0px; margin-top:0px; opacity:0; overflow:hidden; padding:0px; position:absolute; top:0px; width:0px"> The democratisation of next-generation sequencing has vastly increased the availability of sequencing data from metabarcoding. However, to effectively prepare these metabarcoding data for subsequent analysis, researchers must consistently apply several different bioinformatic tools-including those which denoise reads, cluster sequences and assign taxonomic identities. This often creates a bioinformatics bottleneck in workflows for non-specialists due to obstacles around: (a) integrating different tools, (b) the inability to easily modify and rerun bioinformatic pipelines involving non-scripted ('point-and-click') elements and (c) the multiple outputs that may be required of a single dataset (e.g. amplicon sequence variants [ASVs] and operational taxonomic units [OTUs]), which often results in users running pipelines multiple times. Here, we introduce SimpleMetaPipeline, an open-source bioinformatics pipeline implemented in R, which addresses these obstacles. SimpleMetaPipeline integrates the most robust and commonly used existing bioinformatic tools in a single reproducible pipeline, with a streamlined choice of parameters, to generate a sequence data table containing alternative clustering and assignment options. SimpleMetaPipeline accepts demultiplexed paired-end and single reads from multiple sequencing runs. We describe the pipeline and demonstrate how alternative annotations enable the easy implementation of multi-algorithm agreement tests to strengthen inferences. SimpleMetaPipeline represents a valuable addition to the existing library of pipelines, providing easy and reproducible bioinformatics, including a range of commonly desired clustering and assignment options, such as OTUs and ASVs. <p style="border:0px; display:block; height:0px; left:-9999px; margin-bottom:0px; margin-left:0px; margin-right:0px; margin-top:0px; opacity:0; overflow:hidden; padding:0px; position:absolute; top:0px; width:0px">