Billi is a tool developed to identify bubbles in pangenome graphs or assembly graphs that use the bidirected graph or GFA representation. Refer to our preprint for details.

git clone https://github.com/at-cg/billi.git
cd billi
make 

./billi decompose -i inputgraph.gfa > out.txt 

Check here to see the command-line options. The output format is similar to pangene, but we only report the entrance edges along with the direction of traversal. The lines beginning with P denote panbubbles and the ones beginning with H denote hairpins.

./billi decompose -i test/gfa_files/t2-1.gfa > out.txt

Bandage visualisation of t2-1 test graph

The graph contains two nested bubbles. Expect the following output:

P <s6 <s4
P >s1 >s3

See the test folder for other test cases.

• Shreeharsha G Bhat, Daanish Mahajan and Chirag Jain. Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs. BioRxiv