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• Introduction
  • The concept of Long Read Support
  • Contact information
  • System requirements
• Template workflows
  • De Novo Assemble Long Reads and Polish with Short Reads
• Import Nanopore Reads
• De Novo Assemble Long Reads
  • De novo assembly parameters
  • De novo assembly output
• Map Long Reads to Reference
  • Map Long Reads to Reference output
• Polish with Reads
  • Polish with Reads output
• Correct Long Reads
  • Correct Long Reads output
• RNA-Seq Analysis for Long Reads
  • Reads and reference settings
  • Mapping settings
  • Expression settings
  • RNA-Seq Analysis for Long Reads output
• Structural Variant Caller for Long Reads
  • Structural Variant Caller settings
  • Structural Variant Caller output
  • Structural Variant Caller algorithm
• Install and uninstall plugins
  • Installation of plugins
  • Uninstalling plugins
• Bibliography

De Novo Assemble Long Reads

The De Novo Assemble Long Reads tool facilitates the generation of de novo assemblies from long reads. It is based on open source tools: Raven [Vaser and Šikic, 2021] for analysis of Oxford Nanopore reads and Pacific Biosciences CLR reads, and hifiasm [Cheng et al., 2021] for assembly of Pacific Biosciences HiFi reads.

The De Novo Assemble Long Reads tool works best with uncorrected long reads why it is not recommended to run the Correct Long Reads tool beforehand.

To run the De Novo Assemble Long Reads tool, go to:

        Toolbox | Long Read Support () | De Novo Assemble Long Reads ()

Select one or more sequence lists containing long reads.

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Subsections

• De novo assembly parameters
• De novo assembly output

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