Bacterial pangenomics: methods and protocols

by Bacci, Giovanni Fondi, Marco Mengoni, Alessio

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Title Statements

Full title :Bacterial pangenomics : methods and protocols / edited by Alessio Mengoni, Giovanni Bacci, and Marco Fondi.

Summary

This completely revised edition explores novel discoveries in bacterial genomic research, with a focus on technical and computational improvements as well as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequencing methods, the book continues with sections covering methods for deep phylogenetic analysis, the role of metagenomic data in understanding the genomics of the many yet uncultured bacteria, progress in genome-to-phenome inference, as well as computational genomic tools. Written for the highly successful Methods in Molecular Biology series, chapters include the type of practical detail necessary for reproducible results in the lab. Authoritative and up-to-date, Bacterial Pangenomics: Methods and Protocols, Second Edition serves as an ideal guide for both highly qualified investigators in bacterial genomics and for less experienced researchers, including students and teachers, who could use a reference for approaching genomic analysis and genome data.

Edition Statements

Publication Date:2021
Edition:Second edition

Publication Statements

Publisher(s):Humana Press
Place of Publication:New York, NY
Language:eng
Publication Date:2021

Notes

Includes index.

The Physical Object

Description:1 online resource (x, 268 pages) : : illustrations (some color)

Edition Identifiers

ISBN:9781071610992, 1071610996
DOI:10.1007/978-1-0716-1099-2
oclc:on1250314493
LC Classification:QH434
Dewey Decimal:579.3/135

PacBio-Based Protocol for Bacterial Genomes Assembly -- The Illumina Sequencing Protocol and the NovaSeq 6000 System -- Comparative Analysis of Core and Accessory Genes in Co-Expression Network -- Inferring Core Genome Phylogenies for Bacteria -- Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods -- Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes -- Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study -- Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets -- Metagenomic Assembly: Reconstructing Genomes from Metagenomes -- Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes -- Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs) -- Host Trait Prediction from High-Resolution Microbial Features -- Phylogenetic Methods for Genome-Wide Association Studies in Bacteria -- Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN -- A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists -- A Protocol for Teaching Basic Next Gener…