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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Journal JoVE
Génétique
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Journal JoVE Génétique
Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

DOI:
10.3791/62872-v

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12:08 min

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August 20, 2021

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, , , , ,
1Department of Biological Sciences,University of Texas at Dallas, 2Department of Urology,University of Texas Southwestern Medical Center

Chapitres

  • 00:04Introduction
  • 01:00dsDNA Pool Cleanup and Concentration
  • 03:25Sequence the Genome Library
  • 05:14Long (MinION) Reads
  • 06:55Generating Hybrid Genome Assembly
  • 08:34Assessing Assembly Quality
  • 09:34Genome Annotation
  • 10:07Results: Analysis of Extracted DNA and Complete Genome Sequencing of Urinary Bacteria
  • 11:37Conclusion

Summary

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This protocol details a comprehensive approach for the culturing, sequencing, and de novo hybrid genome assembly of urinary bacteria. It provides a reproducible procedure for the generation of complete, circular genome sequences useful in studying both chromosomal and extrachromosomal genetic elements contributing to urinary colonization, pathogenesis, and antimicrobial resistance dissemination.

Tags

Hybrid Genome AssemblyUrinary BacteriaShort-read SequencingLong-read SequencingComplete GenomesGenome ArchitectureMobile Genetic ElementsCulturable BacteriaGenome ContentAdapter LigationFlow Cell PrimingDNA Library PreparationSequencing Run

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