Using Bandage on the command line

• Bandage is a great tool to view assembly graphs.
• It’s used in a GUI, but can also be used on the command line.
• To install for use in the Mac terminal, follow Mac instructions here: https://github.com/rrwick/Bandage

To run

cd ~/Bandage
Bandage.app/Contents/MacOS/Bandage --help
Bandage.app/Contents/MacOS/Bandage image [your gfa file] [output.png]

• Command line info: https://github.com/rrwick/Bandage/wiki/Command-line

Formatting options

Bandage.app/Contents/MacOS/Bandage --helpall

Batch edit gfa files

For editing gfa files in a folder: an example:

for file in ~/just-gfas/*; \
do Bandage.app/Contents/MacOS/Bandage image\
$file ${file}.png \
--lengths \ 
--depth \
--fontsize 6 \
--edgelen 50 \
--toutline 2 \
--minnodlen 50 \
--colour blastsolid; \
done