There are a number of mappers available in Geneious. Some mappers are not bundled with Geneious but may be installed as optional plugins from Tools - Plugins. The best mapper to use may depend on your data. Below is a brief overview of the advantages and disadvantages of some mappers.
Geneious
Advantages:
- Fast
- High sensitivity
- Iterative mode to extend past ends of reference sequence and map ends of reads correctly around indels
- Can discover structural variants
- Supports circular reference sequences (maps correctly around the origin)
- Supports soft trimmed reads
- Can map existing alignments and de novo assembled contigs to reference sequences
Provides progress during mapping
Geneious for RNA Seq
Use this when mapping RNA sequence reads to a genome with introns.
Advantages:
- Can map reads that span existing annotated introns
- Can discover novel introns and map ends of reads correctly around these novel introns
- Can discover fusion genes
- Provides progress during mapping
Disadvantages:
- Novel intron and fusion gene discovery is a little slow
BBMap
Advantages:
- Fast
- High sensitivity
Minimap 2 (available as a plugin for Geneious Prime 2020 and later)
Advantages:
- Handles noisy long read data (PacBio, Minion)
- splice-aware alignment of PacBio or Nanopore cDNA or Direct RNA reads to a reference
- Widely used
- Fast
For more information, see https://github.com/lh3/minimap2/blob/master/README.md
Bowtie2 (available as a plugin)
Advantages:
- Low memory usage
- Widely used
STAR
Advantages:
- Annotates splice variants
Disadvantages:
- Mammal genomes require at least 16GB of RAM, ideally 32G