Map Reads to Reference
This section focuses on the core read mapping algorithm. At the end you can find descriptions of the report.
The mapper has a special mode for reads longer than 500bp. It is possible to mix sequence lists with reads that are shorter and reads that are longer than 500bp for the same mapping. In this case the appropriate mapping algorithm will be applied to each of the sequence lists.
The Map Reads to Reference tool does not support reads longer than 100.000bp and is not recommended for Oxford Nanopore reads.
Subsections
- Selecting the reads
- References and masking
- Mapping parameters
- Mapping paired reads
- Non-specific matches
- Gap placement
- Mapping computational requirements
- Reference caching
- Mapping output options
- Summary mapping report