DADA2 Classification

This project currently houses DADA2 pipelines. There are currently three components to this project:

  1. Pulling SRR data from NCBI archives
  2. Cleaning/filtering in DADA2
  3. Core DADA2 algorithms followed by a brief demonstration of alpha and beta diversity in phyloseq.

To download FASTQ files for a project, we use a recipe that gets SRR data from NCBI given a BioProject ID. The FASTQ files are then ran through the DADA2 recipe that will also perform the cleaning/filtering. The DADA2 algorithm performs error learning, denoising, and clustering into amplicon sequence variants (ASVs). The output of DADA2 is a taxonomy table and ASV table (analogous to an OTU table). This recipe performs a short demonstration of alpha and beta diversity in the phyloseq package.

Public Project owned by Emily • updated 3.4 years ago by Bioinformatics Admin

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