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Welcome to the metabarcoding_QAQC_pipeline wiki!

This pipeline was created for the MURI project to process and do preliminary analysis on eDNA metabarcoding data that was produced using an Illumina MiSeq. This pipeline can be used to process metabarcoding data not affiliated with the project, but will need some tweaking. Check out the guide to using this pipeline on primers other an Mifish, Dloop, and C16/C18.

For test data, visit the Zenodo: https://zenodo.org/record/8303276

Table of Contents:

Dependencies
Preparing Your Data
Docker/Singularity Image
I'm Using New Primers: A Guide (under construction)
Metadata
DADA2 Script Documentation
Preliminary Analysis
Outputs
Running the Pipeline

Overview of Metabarcoding Pipeline:

Step 1: Input Files

Take fastq files from Illumina sequencer and prepare data for pipeline

Step 2: Primer Trimming

Use Cutadapt to trim primer sequences off of paired end sequences

Step 3: QC, Filtering, and Taxonomic Assignment

Use DADA2 to perform quality trimming, filtering, paired-read merging, and more data manipulation. Assign taxonomy using DADA2's naive bayes classifier.

Step 4: Preliminary Analysis

Perform preliminary analysis with pyloseq and quarto.

Step 5: Output Files

Review ouput files.