Sequora 3-20 Prokaryotic Genome Alignment Tutorial

Sequora 3–20 Prokaryotic Genome Alignment Pipeline Tutorial

In this tutorial, I walk through the full Sequora 3–20 pipeline for prokaryotic genome comparison, from initial FASTA file preparation to final phylogenomic visualization.

Sequora is a browser-based bioinformatics pipeline designed to analyze whole bacterial and archaeal genomes using a multi-step workflow, including k-mer filtering, seed-and-extend alignment, and local alignment refinement. The pipeline produces similarity-based outputs, including phylogenomic trees and pairwise similarity networks.

In this video, you’ll learn:

How to prepare and merge genome FASTA files
How each part of the Sequora pipeline works (Parts 1–7)
How to run large-scale genome alignments in the browser
How to interpret phylogenomic trees and similarity networks
Key parameters and practical tips for running the pipeline efficiently

This pipeline is particularly useful for:

Comparative genomics of prokaryotes
Exploring genome similarity and clustering
Rapid analysis without command-line tools

⚠️ Note: Sequora produces maps of similarity, not strictly evolutionary phylogenies. Results may differ from traditional tools depending on parameters and dataset selection.

Видео Sequora 3-20 Prokaryotic Genome Alignment Tutorial канала Gregory Muhs