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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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Snakemake workflows for long-read bacterial genome assembly and evaluation.

Peter Menzel1

  • 1Labor Berlin - Charité Vivantes GmbH, Sylter Str. 2, 13353, Berlin, Germany.

Gigabyte (Hong Kong, China)
|April 9, 2024
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Summary

New Snakemake workflows streamline bacterial genome assembly and evaluation using long-read sequencing data. These automated tools simplify testing various assembly pipelines, ensuring accurate and complete genome analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Advancements in long-read sequencing technologies have increased their application in bacterial genomics.
  • Numerous methods exist for genome assembly from error-prone long reads and subsequent polishing.
  • The variety of available tools creates a complex landscape for users seeking optimal assembly pipelines.

Purpose of the Study:

  • To develop automated workflows for comprehensive genome assembly and evaluation.
  • To simplify the process of testing multiple assembly and polishing strategies.
  • To provide end users with an accessible solution for analyzing bacterial genome data.

Main Methods:

  • Development of two Snakemake-based workflows for automated genome assembly and evaluation.
  • Integration of various assembly and polishing tools within the workflows.
  • Utilization of the conda package manager for simplified program installation.
  • Implementation of assembly quality assessment metrics.

Main Results:

  • The workflows facilitate the simultaneous execution of multiple genome assembly and evaluation programs.
  • Users can easily test diverse combinations of assembly pipelines for their sequencing data.
  • The use of conda eliminates the need for manual installation of individual software packages.
  • Automated evaluation provides insights into the completeness and accuracy of generated assemblies.

Conclusions:

  • The developed Snakemake workflows offer an efficient and user-friendly approach to bacterial genome assembly and analysis.
  • These tools address the need for standardized evaluation of assembly quality.
  • The open-source availability promotes reproducibility and wider adoption in the research community.