Mapping algorithms available in Geneious
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:
Bowtie2
Advantages:
- Low memory usage
- Widely used
Tophat RNA Seq
Advantages:
- Discovers novel introns
- Widely used
Disadvantages:
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