Table 3 Time requirement for each program with a variable number of available nodes to align the simulated dataset
Program | Nodes (cores) | Time required (hh:mm:ss) | Read pairs/core/sec. | Options |
|---|---|---|---|---|
Bismark | 1 (12) | 05:05:32 | 90.91 | -p 5 –bam |
Bison | 1 (12) | 01:29:25 | 310.66 | -p 5 |
Bison | 3 (36) | 00:40:21 | 229.47* | -p 11 |
bison_herd | 1 (12) | 01:35:43 | 290.21 | -p 5 |
bison_herd | 3 (36) | 00:39:21 | 235.30* | -@ 4 –p 11 |
bison_herd | 5 (60) | 00:21:24 | 259.61* | -mp 2 -@ 4 -p 11 |
bison_herd | 9 (108) | 00:13:55 | 221.78* | -mp 2 -@ 4 -p 11 |
BSmooth | 1 (12) | 07:44:02 | 59.86 | -p 5 –no-mixed –no-discordant –no-unpaired |
BSMAP | 1 (12) | 00:15:24 | 1803.75 | -p 12 |
BSMAP | 1 (12) | 00:14:40 | 1898.94 | -p 12 –r 0 |
BS-Seeker2 | 1 (12) | 04:38:07 | 99.88 | –aligner = bowtie2 –bt2-p 6 –bt2–end-to-end |
GNUMAP-bs | 1 (12) | 04:26:53 | 104.08 | –lib_type wt1 –read_type dna –nt_conv bs –-num_threads 12 –skip_blat 1 –pileup 1 –m 22 –a 0.90 |