Polish Contigs with Reads
The Polish Contigs with Reads tool facilitates the process of refining a set of contigs 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 reads to polish the contigs.
Before polishing, the high-quality reads should be stripped of adapters and lower quality bases. This can be done using Trim Reads (Trim Reads).
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 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 Contigs with Reads tool, go to:
Tools | De Novo Sequencing (
) | Polish Contigs with Reads (
)
Select a contig sequence list.
In the next dialog, set the polishing parameters (figure 35.32):
Figure 35.32: Polish Contigs 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