Part I: Opportunities from Novel Sequencing Technologies

1. PacBio-Based Protocol for Bacterial Genomes Assembly

Agata Motyka-Pomagruk, Sabina Zoledowska, Michal Kabza, and Ewa Lojkowska

2. The Illumina Sequencing Protocol and the NovaSeq 6000 System

Part II: Pangenomics of Cultured Isolates

3. Comparative Analysis of Core and Accessory Genes in Co-Expression Network

Biliang Zhang, Jian Jiao, Pan Zhang, Wen-Jing Cui, Ziding Zhang, and Chang-Fu Tian

4. Inferring Core Genome Phylogenies for Bacteria

Alexander Keller and Markus J. Ankenbrand

5. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods

Guillaume Bernard, Timothy G. Stephens, Raúl A. González-Pech, and Cheong Xin Chan

6. Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes

Bernhard Haubold and Fabian Klötzl

7. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study

Sabina Zoledowska, Agata Motyka-Pomagruk, Agnieszka Misztak, and Ewa Lojkowska

Part III: Dark Matter Pangenomics

8. Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets

Chiara Vanni

9. Metagenomic Assembly: Reconstructing Genomes from Metagenomes

Zhang Wang, Jieliang Liang, Linan Huang, Alessio Mengoni, and Wensheng Shu

10. Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes

Davide Albanese and Claudio Donati

11. Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs)

Francesca Di Cesare

12. Host Trait Prediction from High-Resolution Microbial Features

Giovanni Bacci

Part IV: Progresses in Genome-to-Phenome Inference

13. Phylogenetic Methods for Genome-Wide Association Studies in Bacteria

Xavier Didelot

14. Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN

Mikolaj Dziurzynski, Przemyslaw Decewicz, Karol Ciuchcinski, Adrian Gorecki, and Lukasz Dziewit

Part V: Cookbook for Pangenomics

15. A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists

Camilla Fagorzi and Alice Checcucci

16. A Protocol for Teaching Basic Next Generations Sequencing (NG