There are a number of assemblers available in Geneious Prime. Some assemblers are not bundled with Geneious but may be installed as optional plugins from Tools - Plugins. The best assembler to use may depend on your data. Below is a brief overview of the advantages and disadvantages of some assemblers.
Geneious
Advantages:
- Produces large contigs
- Produces contigs containing reads
- Can produce list of unused reads
- Can produce circular contigs
Disadvantages:
- Slow (not feasible to use on genomes over 100 Mbp)
- High memory usage
Tadpole (Geneious R9 onwards)
Advantages:
- Extremely fast
- Very low mis-assembly rate
Disadvantages:
- Produces only consensus sequences
- May produce shorter contigs
- May not work as well on gappy error models (e.g. 454, IonTorrent, PacBio)
- Does not produce scaffolds
SPAdes (Geneious 10.1 onwards)
Advantages:
- Produces long and accurate contigs
- Works with many data types (Note: Oxford Nanopore, PacBio, and Sanger reads can only be used in hybrid assemblies with higher quality short read data).
- Supports RNA and metagenome data
Disadvantages:
- Produces only consensus sequences
- Doesn't work with low coverage
- Not designed for large genomes
Flye (plugin for Prime 2020.1 onwards)
Advantages:
- Fast
- Designed for PacBio and Nanopore data
- Works with metagenome data
Disadvantages:
- Doesn't support short reads (under 1000 bp)
- Produces consensus sequences only
Velvet (plugin)
Advantages:
- Fast
- Widely used
- More efficient on larger genomes than Geneious assembler
Disadvantages:
- Produces only consensus sequences
- May not work as well on gappy error models (e.g. 454, IonTorrent, PacBio)
MIRA (plugin)
Advantages:
- Works very well on bacterial genomes
- Produces large contigs
- Produces contigs containing reads
Disadvantages:
- Not feasible to use on large genomes