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

Andrew Camilli

doi:10.1101/pdb.top107847

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

Cold Spring Harb Protoc. 2023 Jan 3;2023(1):1-3. doi: 10.1101/pdb.top107847.

Author

Andrew Camilli¹

Affiliation

¹ Department of Molecular Biology and Microbiology, Tufts University, School of Medicine, Boston, Massachusetts 02111, USA andrew.camilli@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.

MeSH terms

Bacteria* / genetics
Base Sequence
Genome, Bacterial*
High-Throughput Nucleotide Sequencing / methods
Molecular Sequence Annotation
Phylogeny
Sequence Analysis, DNA / methods
Software

Grants and funding

R37 AI055058/AI/NIAID NIH HHS/United States