Table 3 The runtimes (mean ± SD of three independent runs) and the memory usage of the eight UMI clustering tools on the simulated, reference, and sample data, respectively.
Datasets | Tools | Time (min) – mean (SD) | Memory (GB) | Default parameters |
|---|---|---|---|---|
Simulated data (1.8 M reads) | AmpUMI | 0.12 (± 0.01) | 0.24 | --min_umi_to_keep 0 |
Calib | 0.06 (± 0.005) | 0.07 | -e 2 -k 4 -m 7 -t 3 | |
CD-HIT | 1.45 (± 0.10) | 0.32 | -c 0.90 | |
Du Novo | 0.62 (± 0.08) | 0.09 | -d 1 | |
Rainbow | 0.11 (± 0.02) | 0.07 | -m 4 | |
Starcode | 0.14 (± 0.03) | 0.25 | 0:50:3:3 | |
UMICollapse | 1.58 (± 0.12) | 18.36 | -k 1 -p 0.5 | |
UMI-Tools | 1.64 (± 0.11) | 18.36 | --edit-distance-threshold 1 | |
Reference data (11.3 M reads) | AmpUMI | 1.49 (± 0.15) | 2.59 | --min_umi_to_keep 0 |
Calib | 10.20 (± 1.20) | 1.21 | -e 2 -k 4 -m 7 -t 3 | |
CD-HIT | 231.51 (± 5.30) | 4.14 | -c 0.90 | |
Du Novo | 37.64 (± 2.90) | 6.21 | -d 1 | |
Rainbow | 2.59 (± 0.30) | 0.99 | -m 4 | |
Starcode | 2.08 (± 0.25) | 4.10 | 0:50:3:3 | |
UMICollapse | 44.93 (± 2.40) | 28.13 | -k 1 -p 0.5 | |
UMI-Tools | 43.93 (± 1.50) | 27.86 | --edit-distance-threshold 1 | |
Simple data (16.4 M reads) | AmpUMI | 2.29 (± 0.20) | 3.95 | --min_umi_to_keep 0 |
Calib | 13.94 (± 1.50) | 1.79 | -e 2 -k 4 -m 7 -t 3 | |
CD-HIT | 124.52 (± 8.10) | 6.12 | -c 0.90 | |
Du Novo | 12.63 (± 1.10) | 0.91 | -d 1 | |
Rainbow | 3.55 (± 0.40) | 1.52 | -m 4 | |
Starcode | 3.21 (± 0.35) | 6.21 | 0:50:3:3 | |
UMICollapse | 66.60 (± 3.80) | 25.20 | -k 1 -p 0.5 | |
UMI-Tools | 67.36 (± 2.30) | 24.86 | --edit-distance-threshold 1 |
