• Product manuals

Browse the manual

• 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

Polish with Reads

The Polish with Reads tool facilitates the process of refining a set of sequences with high-quality reads. This enables the creation of hybrid assemblies by first creating an assembly from long, error prone reads, and subsequently using high-quality Illumina reads to polish the contigs.

Before polishing, high-quality reads should be stripped of adapters and lower quality bases. This can be done using Trim Reads (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_Reads.html).

The tool uses Racon [Vaser et al., 2017] with additional improvements inspired by Minipolish [Wick and Holt, 2019]. Racon uses a divide-and-conquer approach for rapid consensus calling. The partial order alignment (POA) of the reads against the target sequences occurs in non-overlapping windows on the target sequences. This approach has the consequence that Racon may not always use a globally optimal alignment of reads for consensus calling.

Polishing is conducted in two steps. Following each step, a set of corrections, inspired by minipolish [Wick and Holt, 2019], are carried out to improve contig quality:

• Contig ends that were truncated by Racon are reintroduced.
• Circular contigs are rotated by half the sequence length in each of the iterations.
• For circular contigs, the mapping is corrected for reads that span the junction.

To run the Polish with Reads tool, go to:

        Toolbox | Long Read Support () | Polish with Reads ()

Select a sequence list containing contigs or long reads.

In the next dialog, set the polishing parameters (figure 6.1):

Figure 6.1: Polish with Reads parameters

• Reads. Select a sequence list of trimmed, high-quality reads to be used for polishing.
• POA window size. The window size for which Racon computes partial order alignments (POA). A larger window size enhances the ability to capture more global structure during the polishing process, but it also increases the memory requirement.
• Include unpolished sequences. Check the checkbox to keep sequences for which polishing was not possible.
• Minimum sequence length. The minimum length of sequences to be included in the output.

---

Subsections

• Polish with Reads output

---