Which map to reference assembly algorithm is best for my data?

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

Bowtie2

      Advantages:
            - Low memory usage
            - Widely used

Tophat RNA Seq

      Advantages:
            - Discovers novel introns
            - Widely used
 
      Disadvantages:
            - Not available on Windows     

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