Using Geneious for microbial genomics and investigating other small sequences

Next generation sequencing (NGS) of small genomes has proved to be an effective tool in microbiology, virology and infectious disease research. Here’s how you can use Geneious to investigate the results from any sequencing technology.

Study diversity with 16s rRNA

Select your microbial species and choose your alignment method, then build a phylogenetic tree based on your alignment.

Discover new microbes

Geneious is great for metagenomic applications. Trim and filter sequences to remove poor-quality sequences.

Investigate large genomic events such as horizontal gene transfer

Align whole genomes with MAUVE.

Bin sequences into clusters using de-novo assembler

Assemble short reads with Velvet. Filter sequences based on length to remove sequences that are too short after trimming.

Find novel or pathogenic mutational variants using re-sequencing

Download a reference sequences and map your microbe against it.

Find genes in microbial DNA


Download bacterial genome annotations

Directly download fully annotated reference genomes.

Design cloning PCR experiments

One-step in-silico molecular cloning and PCR operations. Design primers for areas of interest using Primer3.

Download information on eukaryotic pathogens

Connect Geneious with PlasmoDB and PiroplasmaDB.