Note - great list of genome browsers here: https://github.com/cmdcolin/awesome-genome-visualization

Artemis

Artemis on the desktop

• Install Artemis http://www.sanger.ac.uk/science/tools/artemis
• Load a reference genome - .gbk
• Load a snps file - snps.bam
• This is an alignment of reads against the reference, with snps called by another program (e.g. snippy).
• Zoom L-R using horizontal scroll bar
• Zoom in and out - right-hand vertical scroll bar.
• Reference track:
  • Annotated features are in blocks of colour. E.g. one CDS (blue) might contain many features (green).
  • Select an annotation and see the corresponding reads in the bam file highlighted.
• Bam track:
  • Right-click: show: snps

Artemis on the command line

To see prokka (annotations) output in artemis:

art prokka.gbk

Links

Artemis manual <ftp.sanger.ac.uk/pub/resources/software/artemis/artemis_genome_informatics_2010.pdf>