Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology

Abstract

Background

Amplicon sequencing of phylogenetic marker genes, e.g., 16S, 18S, or ITS ribosomal RNA sequences, is still the most commonly used method to determine the composition of microbial communities. Microbial ecologists often have expert knowledge on their biological question and data analysis in general, and most research institutes have computational infrastructures to use the bioinformatics command line tools and workflows for amplicon sequencing analysis, but requirements of bioinformatics skills often limit the efficient and up-to-date use of computational resources.

Results

We present dadasnake, a user-friendly, 1-command Snakemake pipeline that wraps the preprocessing of sequencing reads and the delineation of exact sequence variants by using the favorably benchmarked and widely used DADA2 algorithm with a taxonomic classification and the post-processing of the resultant tables, including hand-off in standard formats. The suitability of the provided default configurations is demonstrated using mock community data from bacteria and archaea, as well as fungi.

Conclusions

By use of Snakemake, dadasnake makes efficient use of high-performance computing infrastructures. Easy user configuration guarantees flexibility of all steps, including the processing of data from multiple sequencing platforms. It is easy to install dadasnake via conda environments. dadasnake is available at https://github.com/a-h-b/dadasnake.

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Now published in GigaScience doi: 10.1093/gigascience/giaa135

Christina Weiβbecker 1Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil EcologyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Christina WeiβbeckerBeatrix Schnabel 1Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil EcologyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAnna Heintz-Buschart 2German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Bioinformatics Unit1Helmholtz Centre for Environmental Research GmbH - UFZ, Department of Soil EcologyFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anna Heintz-BuschartFor correspondence: anna.heintz-buschart@ufz.de

A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa135 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

These peer reviews were as follows:

Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102503 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102504

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