Table 3 Time- and memory-performance results for decomposing de Bruijn graphs into maximal vertex-disjoint paths
From: Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
Short-read sets | Whole-genome references | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
UST | Cuttlefish 2 | ProphAsm | UST | Cuttlefish 2 | ||||||||
Dataset | k | Thread- count | Default memory | Unrestricted memory | Dataset | k | Thread-count | Default memory | Unrestricted memory | |||
Round-worm | 27 | 1 | 22 min (3.7) | 11 min (2.9) | 09 min (11.2) | Round-worm | 27 | 1 | 03 min (3.9) | 08 min (5.6) | 03 min (2.0) | 03 min (3.1) |
8 | 07 min (3.6) | 02 min (2.9) | 02 min (11.1) | 8 | -- | 02 min (0.8) | 01 min (2.0) | 01 min (2.0) | ||||
55 | 1 | 24 min (3.2) | 19 min (2.9) | 15 min (11.2) | 55 | 1 | 10 min (7.3) | 04 min (2.8) | 04 min (3.9) | |||
8 | 08 min (3.3) | 02 min (2.9) | 02 min (11.2) | 8 | 02 min (1.2) | 01 min (2.8) | 01 min (3.4) | |||||
Gut micro-biome | 27 | 1 | 09 h 02 min (39.2) | 04 h 30 min (3.1) | 04 h 02 min (26.8) | Human | 27 | 1 | 01 h 54 min (91.8) | 03h 59m (38.6) | 01 h 28 min (3.1) | 01 h 29 min (11.2) |
8 | 03 h 10 min (39.2) | 53 min (3.3) | 37 min (26.9) | 8 | -- | 01 h 09 min (10.3) | 14 min (3.2) | 12 min (11.3) | ||||
55 | 1 | 10 h 36 min (34.8) | 06 h 59 min (3.6) | 05 h 51 min (69.9) | 55 | 1 | 04 h 55 min (30.2) | 02 h 16 min (3.2) | 02 h 07 min (11.3) | |||
8 | 03 h 24 min (34.8) | 01 h 13 min (3.8) | 49 min (69.9) | 8 | 01 h 02 min (10.0) | 22 min (3.4) | 19 min (11.2) | |||||
Human | 27 | 8 | 04 h 56 min (13.1) | 01 h 18 min (3.2) | 01 h 01 min (11.3) | |||||||
55 | 04 h 56 min (7.7) | 02 h 29 min (3.5) | 01 h 11 min (11.3) | 7-humans | 27 | 1 | ∗ | 04 h 38 min (20.7) | 01 h 58 min (3.1) | 01 h 46 min (11.2) | ||
8 | -- | 01 h 49 min (20.2) | 18 min (3.2) | 15 min (11.2) | ||||||||
55 | 1 | 05 h 55 min (20.7) | 02 h 48 min (3.4) | 02 h 28 min (11.2) | ||||||||
8 | 01 h 38 min (20.2) | 27 min (3.6) | 21 min (11.2) | |||||||||