De novo assembly parameters
In the dialog seen in figure 4.1, the following parameters are available:
Figure 4.1: De Novo Assemble Long Reads parameters.
- Polish with reads. When this parameter is set, two iterations of read polishing are run on the raw contig output, similar to running Polish with Reads (see Polish with Reads). Disabling this parameter results in raw contigs with error rates similar to the error rate of the reads. This option is disabled for PacBio HiFi reads.
- Minimum contig length. The minimum length of contigs included in the output. Shorter contigs will be filtered.
- Keep circular contigs. When enabled, the minimum contig length filtering is not applied to circular contigs. This means that all circular contigs will be output regardless of length.
- PacBio HiFi options (enabled for PacBio HiFi reads only)
- Genome size. Infer automatically determines the genome size as part of the analysis. Manual instructs the algorithm to use the genome size specified in the text field below for inferring read coverage.
- Genome size (megabases). Enter the expected genome size.
- Ploidy. The number of expected alleles. If it is set to >2, the quality of the assembly for polyploid genomes might be improved.
When running running De Novo Assemble Long Reads in a workflow, the workflow element dialog will contain an additional option:
- PacBio HiFi. Check this option to indicate that input reads are PacBio HiFi reads. When selected, the tool will run with an algorithm optimized for HiFi reads.
When running the De Novo Assemble Long Reads tool separately, the read type is inferred from the input reads.