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\(\times \)
Tool
Time
RAM (MB)
Yeast
ABySS unitig
00:00:11:03
2283
ABySS full
00:00:20:01
2283
\({\sim} 5\times \)
Mapping
00:00:00:05
540
LazyB
00:00:00:30
136
A+m+ LazyB
00:00:11:38
2283
Canu
00:10:23:55
2617
Wtdbg2
00:00:13:08
698
HASLR
00:00:06:44
4922
DBG2OL
00:00:31:46
1141
Wengan
00:00:06:45
4400
A+Wengan
00:00:26:46
4400
\({\sim} 11\times \)
Mapping
00:00:00:15
1544
LazyB
00:00:01:46
362
A+m+ LazyB
00:00:13:04
2283
Canu
00:13:44:16
6779
Wtdbg2
00:00:29:28
1142
HASLR
00:00:08:09
4922
DBG2OL
00:00:51:13
1264
Wengan
00:00:14:29
4421
A+Wengan
00:00:34:30
4421
Fruit fly
ABySS untig
00:02:32:39
25344
ABySS full
00:04:56:03
25346
\({\sim} 5\times \)
Mapping
00:00:02:43
6433
LazyB
00:00:08:33
613
A+m+ LazyB
00:02:43:55
25344
Canu
02:13:51:39
7531
Wtdbg2
00:01:37:41
3395
HASLR
00:01:30:33
5531
DBG2OL
00:07:58:22
6151
Wengan
00:01:41:26
5394
A+Wengan
00:06:10:29
25346
\({\sim} 10\times \)
Mapping
00:00:06:11
9491
LazyB
00:00:11:57
2241
A+m+ LazyB
00:02:50:47
25344
Canu
07:04:08:28
7541
Wtdbg2
00:04:02:43
5024
HASLR
00:01:43:21
5553
DBG2OL
02:07:32:01
17171
Wengan
00:02:28:51
5323
A+Wengan
00:07:24:54
25346
Step (1) is often not needed as short-read assemblies are available for many organisms
Similarly, Wengan requires a full ABySS assembly as a its basis. Resources are only compared for yeast and fruit fly, because Canu cannot be run for human in acceptable time and resource-constraints on our equipment. As all tools except LazyB and DBG2OL are parallelized, running times are given as the sum of time spent by all CPUs. Therefore, computational effort is measured rather than wallclock time. ABySS greatly dominates the LazyB pipeline and to a lesser degree also Wengan . Nevertheless, LazyB is faster by a factor of \(>60\) compared to Canu , \(\approx 3\) compared to DBG2OL , and \(\approx 2.5\) to Wengan
