Bacterial Pangenomics: Methods and Protocols

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