Titlebook: Bacterial Pangenomics; Methods and Protocol Alessio Mengoni,Giovanni Bacci,Marco Fondi Book 2021Latest edition Springer Science+Business Me

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PacBio-Based Protocol for Bacterial Genome Assemblyelopment of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline ba

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The Illumina Sequencing Protocol and the NovaSeq 6000 Systeme typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Several types of sequencing kits coupled with dual flow cell mode enable high scalability of se

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Inferring Core Genome Phylogenies for Bacteriaed on more than a single or few marker genes have become feasible. In this method protocol, we describe the complete bioinformatic workflow from raw genomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions

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Fast Phylogeny Reconstruction from Genomes of Closely Related Microbesge in technology is leading to the rapid accumulation of large samples of closely related genome sequences. Summarizing such samples into phylogenies can be computationally challenging. Our program . quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working u

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Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Studyassembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were app

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Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets information has the potential to widen our understanding of the functioning of microbial communities and their roles in the environment. A fundamental step in this process is the functional and taxonomic profiling of the metagenomes, through an accurate gene annotation. This gene-level information

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Metagenomic Assembly: Reconstructing Genomes from Metagenomesional capacity of microorganisms. The rapid development of sequencing technology and novel assembly algorithms have made it possible to reliably reconstruct hundreds to thousands of microbial genomes from raw sequencing reads through metagenomic assembly. In this chapter, we introduce a routinely us

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Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomesarches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.