Map Long Reads to Reference
The Map Long Reads to Reference tool enables aligning long reads to a reference with minimap2 [Li, 2018].
To run the tool, go to:
Tools | Resequencing Analysis (
) | Map Long Reads to Reference (
)
Select one or more sequence lists containing long reads.
In the following step, select one or more reference sequences. You can select either individual sequences, a list of sequences or a sequence track as reference (figure 30.12).
Figure 30.12: Map Long Reads to Reference reference selection.
In the Mapping options dialog, set the read mapping parameters (figure 30.13):
Figure 30.13: Map Long Reads to Reference mapping options.
- Mapping mode. Choose between the following modes for parameter setting:
- Automatic. Match cost parameters are set automatically based on the read type of the first input (e.g. Oxford Nanopore or Pacbio HiFi).
- Automatic spliced. Similar to Automatic, except it generates spliced alignments, which can be useful for visualizing RNA-seq data.
- Manual. Allows match costs to be specified manually. This will overwrite the read type specific match costs that would otherwise be used with the values entered below.
- Match score. Score of a match.
- Mismatch cost. Cost of a mismatch.
- Gap open cost. Cost of starting a gap.
- Gap extend cost. Cost of extending a gap.
- Long gap open cost. Cost of starting a long gap. Long gaps are typically more expensive to open but cheaper to extend. The alignment will use the cheaper alternative.
- Long gap extend cost. Cost of extending a long gap.
- Score bonus for global alignment. A bonus that may be added to the alignment score if the alignment encompasses all nucleotides of the read.
For guidance on adjusting match cost parameters, see Mapping parameters. Additional information on parameters are available from the minimap2 documentation.
Subsections