Note - great list of genome browsers here: https://github.com/cmdcolin/awesome-genome-visualization
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:
Artemis on the command line
To see prokka (annotations) output in artemis:
Artemis manual <ftp.sanger.ac.uk/pub/resources/software/artemis/artemis_genome_informatics_2010.pdf>