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Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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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
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Recycler: an algorithm for detecting plasmids from de novo assembly graphs.

Roye Rozov1, Aya Brown Kav2, David Bogumil2

  • 1Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.

Bioinformatics (Oxford, England)
|December 23, 2016
PubMed
Summary
This summary is machine-generated.

Recycler is a new algorithm that accurately assembles circular elements like plasmids from microbial sequencing data. This tool enhances the recovery of true plasmids, aiding research in antibiotic resistance and metabolite production.

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Area of Science:

  • Genomics and Bioinformatics
  • Microbial Evolution
  • Molecular Biology

Background:

  • Plasmids and mobile genetic elements drive microbial evolution and genome innovation.
  • These elements are crucial in antibiotic resistance and metabolite production for industry.
  • Characterizing circular elements via deep sequencing remains a significant bioinformatics challenge.

Purpose of the Study:

  • To develop a novel algorithm for assembling circular elements from microbial sequencing data.
  • To improve the accurate recovery and characterization of plasmids, phages, and other circular DNA molecules.

Main Methods:

  • Introduced Recycler, a circular element assembly algorithm.
  • Leveraged assembly graphs from de novo assemblers and paired-end read alignments.
  • Applied to isolate microbial genomes, plasmidomes, and metagenomes.

Main Results:

  • Recycler is the first tool to extract complete circular contigs from diverse microbial sequence data.
  • Significantly increased true plasmid recovery compared to existing methods with high accuracy.
  • Experimental validation confirmed high accuracy (89% mean) across isolate, microbiome, and plasmidome data.

Conclusions:

  • Recycler effectively addresses the challenge of assembling circular elements from sequencing data.
  • Provides a robust and accurate method for plasmid and mobile element characterization.
  • Facilitates advancements in understanding microbial evolution, antibiotic resistance, and biotechnology applications.