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Table 5 Assessment of running times for all tools. Resource consumptions for LazyB are shown for the complete assembly process comprising (1) ABySS unitig assembly; (2) Mapping of unitigs to long reads and (3) running LazyB itself, denoted by A+m+ LazyB, and the the last step only, denoted by LazyB

From: LazyB: fast and cheap genome assembly

\(\times \) 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
  1. Step (1) is often not needed as short-read assemblies are available for many organisms
  2. 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