Bacterial Pangenomics

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 Generations Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R.