• Product manuals

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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

System requirements

Long Read Support 24.0 is for use with CLC Genomics Workbench 24.0 or newer. The system requirements for CLC Genomics Workbench are provided at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=System_requirements.html

The system requirements for Long Read Support are the same as those for CLC Genomics Workbench, apart from the following:

• An AMD/Intel CPU that supports AVX2 or an Apple M series CPU is required for the below tools:
  • Polish with Reads
  • Correct Reads
  • De Novo Assemble Long Reads

Special requirements when assembling PacBio HiFi reads with De Novo Assemble Long Reads

At least 32 GB RAM is recommended for running the De Novo Assemble Long Reads tool with PacBio HiFi reads.

Special requirements for Correct Reads and Polish with Reads

Correct Reads and Polish with Reads use Racon [Vaser et al., 2017] for which the follwing is listed:

• Memory consumption of polishing equals the size of the mandatory input files, while the memory is somewhat larger for error correction. (https://complex.zesoi.fer.hr/en/blog-en/58-racon-1-0-release)

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