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:

Geneious for RNA Seq

Use this when mapping RNA sequence reads to a genome with introns.

Advantages:

Disadvantages:

BBMap

Advantages:

Bowtie2

Advantages:

Tophat RNA Seq

Advantages:

Disadvantages:

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