Assembly annotation tutorial for Porecamp 2016

An easy way to annotate an assembly is to run prokka. The default database is set up for microbes, so we could annotate an E coli assembly.

Once you have a de novo assembly, all you have to do is run prokka to generate the GenBank format files (.gbk) containing the annotation.

prokka --outdir Ecoli_annot --prefix Ecoli.pass prokka Ecoli.pass.contigs.fa

How have a look at the output files to see what was found.

How many genes were found (in the PREFIX.txt file)?

It would be great to visualise the data. programs like DNAPlotter or Circos would be useful for visualising, but might require some programming to produce these sorts of impressive diagrams.