README.md

MURI Metabarcoding Pipeline

This pipeline performs metabarcoding analysis using Cutadapt and DADA2. For more information on usage and dependencies, visit the wiki: https://github.com/MMARINeDNA/metabarcoding_QAQC_pipeline/wiki

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

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.