Pulsed Field Gel Electrophoresis and Genome Size Estimates -- Comparative Analyses of Extrachromosomal Bacterial Replicons, Identification of Chromids and Experimental Evaluation of their Indispensability -- Choice of Next Generation Sequencin Pipelines -- The Pyrosequencing Protocol for Bacterial Genomes -- Bacterial Metabarcoding by 16S rRNA Gene Ion Torrent Amplicon Sequencing -- The Ilumina-Solexa Sequencing Protocol for Bacterial Genomes -- High-Throughput Phenomics -- Comparative Analysis of Gene Expression: Uncovering Expression Conservation and Divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S -- Raw Sequence Data and Quality Control -- Methods for Assembling Reads and Producing Contigs -- Mapping Contigs Using CONTIGuator -- Gene Calling and Bacterial Genome Annotation with BG7 -- Defining Orthologs and Pangenome Size Metrics -- Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids -- Genome-Scale Metabolic Networks Reconstruction -- From Pangenome to Phanphenome and Back -- Genome-Wide Detection of Selection and Other Evolutionary Forces -- The Integrated Microbial Genome Resource of Analysis.

Bacterial genomics is a mature research interdisciplinary field, which is approached by ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, industrial and basic science.  Thanks to the large diffusion of bacterial genome analysis , Bacterial Pangenomics: Methods and Protocols is able to provide the most recent methodologies about the study of bacterial pangenomes by covering the three major areas: the experimental methods for approaching bacterial pangenomics, the bioinformatic pipelines for analysis and annotation of sequence data, and finally the methods for inferring functional and evolutionary features from the pangenome. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.   Authoritative and easily accessible, Bacterial Pangenomics: Methods and Protocols will serve as a field guide for both qualified bacterial genomics investigators who want to update their technical knowledge, for less experienced researchers who want to start working with bacterial genomics and pangenomics, as well as serving as a manual and supplemental textbook for graduate students of genomics and bioinformatics.