From: Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
ABySS-Bloom-dBG | Bifrost | deGSM | BCALM 2 | CUTTLEFISH 2 | ||||||
---|---|---|---|---|---|---|---|---|---|---|
Dataset | k | Thread-count | Small-memory | Large-memory | Default memory | Match second-best memory | Unrestricted memory | |||
Human | 27 | 8 | 22 h 18 min (39.3) | 20 h 23 min (71.3) | 11 h 43 min (48.5) | 10 h 36 min (235.8) | 04 h 23 min (6.7) | 01 h 13 min (3.2) | 01 h 10 min (6.2) | 01 h (11.3) |
16 | 11 h 38 min (39.3) | 11 h 02 min (71.3) | 09 h 39 min (48.6) | 07 h 08 min (235.8) | 04 h 58 min (8.9) | 56 min (3.3) | 56 min (7.6) | 51 min (11.3) | ||
55 | 8 | 16 h 32 min (34.0) | 15 h 58 min (66.0) | 05 h 43 min (43.8) | 16 h 50 min (293.2) | 04 h 01 min (7.4) | 02 h 20 min (3.5) | 01 h 08 min (7.1) | 01 h 03 min (11.3) | |
16 | 09 h 28 min (34.1) | 08 h 37 min (66.1) | 04 h 16 min (43.9) | 15 h 54 min (293.3) | 04 h 26 min (10.5) | 02 h 02 min (3.7) | 01 h 11 min (9.5) | 51 min (11.3) | ||
Human RNA-seq | 27 | 8 | 11 h 47 min (33.7) | 11 h 22 min (65.7) | 06 h 04 min (7.2) | 01 h 35 min (87.1) | 02 h 58 min (3.8) | 30 min (2.9) | – | 18 min (80.1) |
16 | 11 h 38 min (39.3) | 07 h 38 min (65.7) | 07 h 24 min (7.2) | 01 h 37 min (87.2) | 02 h 46 min (3.9) | 20 min (3.0) | – | 12 min (80.1) | ||
Gut microbiome | 27 | 16 | 18 h 47 min (42.0) | 20 h 12 min (74.0) | 03 h 54 min (38.1) | 02 h 28 min (157.2) | 02 h 34 min (7.7) | 26 min (3.5) | 23 min (6.7) | 20 min (26.8) |
55 | 1 day 17 h 43 min (35.9) | 1 day 08 h 09 min (67.8) | 02 h 44 min (46.7) | 06 h 53 min (293.3) | 03 h 02 min (12.5) | 44 min (4.0) | 25 min (11.3) | 20 min (69.9) | ||
Soil | 27 | 16 | 1 d 18 h 35 min (150.4) | 14 h 24 min (275.0) | 15 h 28 min (274.1) | 1 day 14 h 29 min (235.8) | 19 h 39 min (52.0) | 02 h 01 min (19.2)) | 02 h 18 min (40.9) | 01 h 35 min (40.9) |
55 | 07 h 57 min (128.9) | 06 h 36 min (256.8) | 05 h 49 min (157.0) | 1 day 11 h 05 min (293.3) | 08 h 30 min (27.5) | 03 h 02 min (11.1) | 02 h 43 min (23.3) | 01 h 38 min (23.3) | ||
White spruce | 27 | 16 | ∗ | X | X | †| 2 days 06 h 12 min (36.8) | 10 h 05 min (14.0) | 07 h 47 min (35.2) | 07 h 13 min (204.2) |
55 | ∗ | X | X | †| 2 days 09 h 59 min (31.6) | 10 h 12 min (23.8) | 10 h 08 min (31.1) | 07 h 24 min (279.3) |