Visualization of PROKKA Annotation Result?

Question

[ferdinand]

Hey everyone, so I have an annotation result of bacteria genome from PROKKA. I need to present it in a more readable format instead of just thousands of rows of gene names. Is there a tool I can use to do this? thanks.

[Joe]

Colin's answer is essentially the right one I believe, but the more immediate consideration is: what are you actually trying to show?

Most bacterial genomes are going to be several megabases at least, with most genes averaging about 1 kilobase - consequently, any attempt to visualise the entire annotation map in one go will be completely meaningless as the scales don't play nicely together.

I assume you're interested in some sub-feature, or some abstractable characteristic, so think about visualising this, rather than the genome.

Answer 1

[colindaven]

You need a genome browser and you can probably use GBK or gff3 format.

Here are some suggestions - I like JBrowse best, Artemis in its day was excellent for bacteria but it is no longer maintained.

• JBrowse
• https://www.sanger.ac.uk/project/artemis/
• Ugene https://github.com/ugeneunipro/ugene
• IGV