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

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1064-3745 expertsThis 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 sequ

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Fritz Böhle,G. Günter Voß,Günther Wachtlercan be computationally challenging. Our program . quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working under the UNIX command line, we show how . can be used to transform genomes to phylogenies with support values ready to be printed or integrated into documents.

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Inferring Core Genome Phylogenies for Bacteriaenomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions with high resolution on strain level or across taxa spanning different clades of the bacterial tree of life.

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Fast Phylogeny Reconstruction from Genomes of Closely Related Microbescan be computationally challenging. Our program . quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working under the UNIX command line, we show how . can be used to transform genomes to phylogenies with support values ready to be printed or integrated into documents.

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The Illumina Sequencing Protocol and the NovaSeq 6000 Systemquencing outputs to match a wide range of applications from complete genome sequencing to metagenomics analysis. In this chapter, after explaining how to assemble a normalized pool of libraries for sequencing, we will describe the experimental steps required to run the pools on the NovaSeq 6000 platform.

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Metagenomic Assembly: Reconstructing Genomes from Metagenomesed metagenomic assembly workflow including read quality filtering, assembly, contig/scaffold binning, and postassembly check for genome completeness and contamination. We also describe a case study to reconstruct near-complete microbial genomes from metagenomes using our workflow.