1. Pulsed Field Gel Electrophoresis and Genome Size Estimates
Rosa Alduina and Annalisa Pisctiotta
2. Comparative Analyses of Extrachromosomal Bacterial Replicons, Identification of Chromids and Experimental Evaluation of their Indispensability
Lukasz Dziewit and Dariusz Bartosik
3. Choice of Next Generation Sequencin Pipelines
Federica Del Chierico, Massimo Ancora, Maurilia Marcacci, Cesare Cammà, Lorenza Putignani, and Salvatore Conti
4. The Pyrosequencing Protocol for Bacterial Genomes
Ermanno Rizzi
5. Bacterial Metabarcoding by 16S rRNA Gene Ion Torrent Amplicon Sequencing
Elio Fantini, Giulio Gianese, Giovanni Giuliano, and Alessia Fiore
6. The Ilumina-Solexa Sequencing Protocol for Bacterial Genomes
Zhenfei Hu, Lei Cheng, and Hai Wang
7. High-Throughput Phenomics
Carlo, Viti, Francesca Decorosi, Emmanuela Marchi, Marco Galardini, and Luciana Giovannetti
8. Comparative Analysis of Gene Expression: Uncovering Expression Conservation and Divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S
Paolo Sonego, Pieter Meysman, Marco Moretto, Roberto Viola, Kris Laukens, Duccio Cavalieri, and Kristof Engelen
9. Raw Sequence Data and Quality Control
Giovanni Bacci
10. Methods for Assembling Reads and Producing Contigs
Valerio Orlandini, Marco Fondi, and Renato Fani
11. Mapping Contigs Using CONTIGuator
Marco Galardini, Alessio Mengoni, and Marco Bazzicalup
12. Gene Calling and Bacterial Genome Annotation with BG7
Raquel Tobes, Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Evdokim Kovach, Alexey Alekhin, and Eduardo Pareja
13. Defining Orthologs and Pangenome Size Metrics
Emanuele Bosi, Renato Fani, and Marco Fondi
14. Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids
Pablo Vinuesa and Bruno Contreras-Moreira
15. Genome-Scale Metabolic Networks Reconstruction
Marco Fondi and Pietro Liò
16. From Pangenome to Phanphenome and Back
Marco Galardini, Alessio Mengoni, and Stefano Mocali
17. Genome-Wide Detection of Selection and Other Evolutionary Forces
Zhuofei Xu and Rui Zhou
18. The Integrated Microbial Genome Resource of Analysis
Alice Checcucci and Alessio Mengoni
