A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Table 3 Space in bytes per input base pair for the explicit and the implicit representation of the compressed de Bruijn graph

k	ds	40 E. coli	62 E. coli	7 × Chr1	7 × HG
50	Explicit	1.80	1.89	2.80	2.57
50	Implicit	0.84	0.82	0.77	0.76
50	Implicit-c1	0.55	0.53	0.47	0.47
50	Implicit-c2	0.30	0.27	0.25	0.26
100	Explicit	1.46	1.51	2.55	2.12
100	Implicit	0.80	0.79	0.75	0.74
100	Implicit-c1	0.51	0.50	0.46	0.45
100	Implicit-c2	0.26	0.24	0.23	0.24
500	Explicit	1.07	1.08	2.50	2.01
500	Implicit	0.74	0.74	0.75	0.74
500	Implicit-c1	0.44	0.44	0.45	0.44
500	Implicit-c2	0.20	0.18	0.23	0.23

The numbers for the explicit representation include the input and the numbers for the implicit representation include the \(\mathsf {BWT}\) stored in a wavelet tree. The suffix -c1 means that the bit vectors \(B_{l}\) and \(B_{r}\) of the implicit representation are compressed, and the suffix -c2 means that additionally the (bit vectors in the) wavelet tree are compressed

ISSN: 1748-7188