Nanopore amplicon analysis manual

Introduction

Welcome to the Nanopore amplicon analysis manual. This documentation covers the NAAM workflow: an amplicon-based pipeline designed for performing quality control, generating consensus sequences, and comparing sequences to references.

This manual is divided into two parts:

1. Quick Start: How to set up and run the automated pipeline immediately.
2. Manual Execution: A detailed breakdown of the underlying bioinformatic steps (Under the hood).

Workflow Summary

The pipeline performs the following steps:

1. Quality control
   • Merging and decompressing raw data.
   • Quality trimming with fastp.
   • Primer trimming with Ampliclip.
2. Generating consensus sequences
   • Mapping trimmed reads to a reference with minimap2.
   • Generate consensus sequences with Virconsens.
3. Comparing sequences to references
   • Create multiple sequence alignment between consensus sequences and a reference.
   • Generate read statistics for raw, QC, trimmed, and mapped reads.
4. Variant Analysis (Optional)
   • Nextclade CLI analysis for clade assignment and mutation calling.