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

 

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

 

Tophat RNA Seq (available as a plugin)

Advantages:

  • Discovers novel introns
  • Widely used

Disadvantages:

  • Not available on Windows
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