Topic Introduction

De Novo Genome Sequencing, Annotation, and Taxonomy of Unknown Bacteria

  1. Andrew Camilli1
  1. Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts 02111, USA
  1. ↵1Correspondence: andrew.camilli{at}tufts.edu

Abstract

Whole-genome sequencing of viruses and bacteria has become routine thanks to advances in DNA-sequencing technologies. Parallel advances in computing power and software design allow for billions of base pairs of sequence information to be analyzed in hours to minutes. Here, I describe methods to isolate known as well as new species of bacteria from the environment; to purify, sequence, assemble, and bioinformatically annotate their genomes; and to determine their place in the tree of life by phylogenetic analysis. The protocol introduced here was developed as part of Cold Spring Harbor's Advanced Bacterial Genetics course.

Footnotes

  • From the Experiments in Bacterial Genetics collection, edited by Lionello Bossi, Andrew Camilli, and Angelika Gründling.

Articles citing this article

  • Selection of Antibiotic-Resistant Bacterial Strains and Identification of Genomic Alterations by Whole-Genome Sequencing: Using Staphylococcus aureus and Oxacillin Resistance as an Example Cold Spring Harb Protoc; 2023;
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This Article

  1. Published in Advance October 25, 2022, doi: 10.1101/pdb.top107847 Cold Spring Harb Protoc © 2022 Cold Spring Harbor Laboratory Press
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