This directory contains a Dockerfile to automatically benchmark bamtocov, covtobed,
mosdepth and megadepth using a set of BAM files.
The image should be build from the root directory.
The first four datasets are available on Zenodo,
where they are downloaded from by the Dockerfile
| Command |
Mean [s] |
Min [s] |
Max [s] |
Relative |
covtobed 'HG00258.bam' #1.3.5 |
563.326 ± 8.611 |
555.070 |
574.771 |
3.25 ± 0.05 |
bamtocov 'HG00258.bam' #2.5.0 |
363.811 ± 8.651 |
350.075 |
373.599 |
2.10 ± 0.05 |
megadepth --coverage 'HG00258.bam' #1.1.2 |
173.520 ± 0.228 |
173.290 |
173.810 |
1.00 ± 0.00 |
megadepth --coverage --longreads 'HG00258.bam' #1.1.2 |
173.281 ± 0.478 |
172.890 |
173.919 |
1.00 |
mosdepth mosdepth.pMD4Cm 'HG00258.bam' #0.3.3 |
469.604 ± 0.839 |
468.725 |
471.000 |
2.71 ± 0.01 |
mosdepth --fast-mode mosdepth.pMD4Cm 'HG00258.bam' #0.3.3 |
459.380 ± 1.134 |
458.283 |
461.134 |
2.65 ± 0.01 |
- Fungal genome WGS, short reads (SR)
| Command |
Mean [s] |
Min [s] |
Max [s] |
Relative |
covtobed 'cpara-illumina-noseq.bam' #1.3.5 |
14.553 ± 0.246 |
14.289 |
14.895 |
3.70 ± 0.10 |
bamtocov 'cpara-illumina-noseq.bam' #2.5.0 |
10.774 ± 0.144 |
10.550 |
10.939 |
2.74 ± 0.07 |
megadepth --coverage 'cpara-illumina-noseq.bam' #1.1.2 |
3.932 ± 0.077 |
3.842 |
4.030 |
1.00 |
megadepth --coverage --longreads 'cpara-illumina-noseq.bam' #1.1.2 |
4.129 ± 0.112 |
4.012 |
4.313 |
1.05 ± 0.04 |
mosdepth mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3 |
11.090 ± 0.135 |
10.908 |
11.289 |
2.82 ± 0.07 |
mosdepth --fast-mode mosdepth.X0pr36 'cpara-illumina-noseq.bam' #0.3.3 |
9.387 ± 0.074 |
9.291 |
9.468 |
2.39 ± 0.05 |
- Fungal genome WGS, long reads (LR)
| Command |
Mean [ms] |
Min [ms] |
Max [ms] |
Relative |
covtobed 'cpara-ont-noseq.bam' #1.3.5 |
494.1 ± 14.3 |
479.1 |
512.8 |
2.09 ± 0.11 |
bamtocov 'cpara-ont-noseq.bam' #2.5.0 |
236.3 ± 10.7 |
224.2 |
253.5 |
1.00 |
megadepth --coverage 'cpara-ont-noseq.bam' #1.1.2 |
400.3 ± 11.5 |
387.4 |
419.2 |
1.69 ± 0.09 |
megadepth --coverage --longreads 'cpara-ont-noseq.bam' #1.1.2 |
406.4 ± 11.4 |
392.1 |
424.8 |
1.72 ± 0.09 |
mosdepth mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3 |
664.9 ± 29.3 |
629.0 |
687.7 |
2.81 ± 0.18 |
mosdepth --fast-mode mosdepth.XMG5Wi 'cpara-ont-noseq.bam' #0.3.3 |
542.8 ± 10.0 |
535.5 |
560.0 |
2.30 ± 0.11 |
- Targeted gene panel (human)
| Command |
Mean [ms] |
Min [ms] |
Max [ms] |
Relative |
covtobed 'panel_01.bam' #1.3.5 |
422.6 ± 3.7 |
417.5 |
427.5 |
2.21 ± 0.06 |
bamtocov 'panel_01.bam' #2.5.0 |
191.3 ± 4.9 |
185.7 |
204.4 |
1.00 |
megadepth --coverage 'panel_01.bam' #1.1.2 |
6068.9 ± 36.9 |
6021.0 |
6121.8 |
31.72 ± 0.83 |
megadepth --coverage --longreads 'panel_01.bam' #1.1.2 |
6050.0 ± 19.7 |
6023.0 |
6078.5 |
31.63 ± 0.81 |
mosdepth mosdepth.zCQZhW 'panel_01.bam' #0.3.3 |
42686.6 ± 7201.3 |
35745.8 |
51457.9 |
223.14 ± 38.07 |
mosdepth --fast-mode mosdepth.zCQZhW 'panel_01.bam' #0.3.3 |
25916.5 ± 166.2 |
25730.0 |
26144.3 |
135.47 ± 3.55 |
| Command |
Mean [s] |
Min [s] |
Max [s] |
Relative |
covtobed 'w1118_f_hd_R1.bam' #1.3.5 |
1.530 ± 0.021 |
1.502 |
1.556 |
2.50 ± 0.06 |
bamtocov 'w1118_f_hd_R1.bam' #2.5.0 |
1.432 ± 0.074 |
1.375 |
1.523 |
2.34 ± 0.13 |
megadepth --coverage 'w1118_f_hd_R1.bam' #1.1.2 |
0.613 ± 0.013 |
0.604 |
0.634 |
1.00 |
mosdepth mosdepth.7dbdyA 'w1118_f_hd_R1.bam' #0.3.3 |
2.939 ± 0.017 |
2.913 |
2.958 |
4.80 ± 0.10 |
mosdepth --fast-mode mosdepth.7dbdyA 'w1118_f_hd_R1.bam' #0.3.3 |
2.907 ± 0.030 |
2.881 |
2.953 |
4.74 ± 0.11 |