Metabarcoding 1: Cucumber Fermentation Microbiome Time Series Data

A 158 MB workshop dataset provides a subsampled cucumber fermentation time series sequenced on an Illumina NextSeq 2000. Alise Ponsero created this resource to demonstrate the DADA2 pipeline for processing 16S rRNA amplicon data from trimmed FASTQ files to annotated ASV count tables. The dataset includes R Markdown notebooks guiding users through quality filtering, error modeling, denoising, and taxonomy assignment using the SILVA 138 reference database.

Use Cases

• Learn quality filtering and trimming steps based on described inspection of quality profiles and truncation parameter selection.
• Practice error rate modeling for Illumina NextSeq/NovaSeq data based on the described use of a custom error function for binned quality scores.
• Execute denoising and chimera removal workflows based on the described steps of running dada(), merging paired-end reads, and constructing a sequence table.
• Assign taxonomy to Amplicon Sequence Variants (ASVs) based on the described use of the naive Bayesian classifier with the SILVA 138 database.

Strengths

• Dataset is specifically designed for a hands-on workshop, providing structured learning blocks with precomputed outputs for computationally intensive steps.
• Includes raw sequencing data from a defined experimental context: a cucumber fermentation time series sequenced on an Illumina NextSeq 2000 with V3-V4 region primers.
• Released under a permissive CC-BY-4.0 license, allowing for broad reuse and modification.

Limitations

• The dataset has been subsampled for workshop speed, which may limit its utility for full-scale analysis.
• Column-level documentation is absent; field semantics must be inferred from the workshop notebooks after download.
• Row count is unknown, which may limit suitability assessment for specific analytical needs.

Provenance

Source

figshare

Collection Method

16S rRNA amplicon sequencing of a cucumber fermentation time series on an Illumina NextSeq 2000, with primer trimming performed in advance.

Freshness

Last updated 2026-05-24 08:45:57; freshness should be verified.