## Comparison of available primary assemblers from long reads Benchmarking - Setonix HPC performance, using the flollowing settings on Slurm: * ```--exclusive``` - used exclusive node for benchmarking * ```--cpus-per-task=24``` * ```--nodes=1``` * ```--ntasks=1``` * ```--partition=work``` * ```--mem=200G``` - maximum memory for work queue | Assembler | Wall-clock time | CPU time | Memory Utilized | |------------------|-----------------|------------|-----------------| | CANU | 04:52:07 | 4-15:32:44 | 62.21 GB | | Flye | 03:36:25 | 2-15:27:51 | 48.03 GB | | NextDenovo | 00:23:12 | 22:00:24 | 159.06 GB | | Wtdbg2 (redbean) | 00:33:29 | 12:27:42 | 6.19 GB | | Raven | 04:37:46 | 4-02:00:55 | 73.81 GB | | Unicycler - lr | NA | NA | > 890 GB | Assembly contiguity and stats for test sample: | Assembler | # of contigs | N50 | min | max | Genome size | |------------------|--------------|--------|-------|--------|-------------| | CANU | 53 | 2619752| 1573 | 4510360| 42.37e6 | | Flye | 422 | 211792 | 574 | 1031083| 38.88e6 | | NextDenovo | 9 | 125536 | 82914 | 170627 | 1076432 | | Wtdbg2 (redbean) | 209 | 595416 | 3277 | 1338536| 36.82e6 | | Raven | 177 | 689747 | 11657 | 4191860| 45.38e6 | | Unicycler - lr | NA | NA | NA | NA | NA | * GoldRush does not work with reads missing Phred quality scores, thus cannot be used for RSII reads PB. * Unicycler runs our of memory, thus not considered here for assembly. ## Comparison for hybrid assemblers | Assembler | Wall-clock time | CPU time | Memory Utilized | |------------------|-----------------|------------|-----------------| | Spades | 03:45:11 | 2-22:34:13 | 18.24 GB | | Unicycler - lr + sr | NA (time-out) | NA | NA | Assembly contiguity and stats for test sample: | Assembler | # of contigs | N50 | min | max | Genome size | |------------------|--------------|--------|-------|--------|-------------| | Spades | 28688 | 342047 | 500 | 1121776| 38.57e6 | | Unicycler - lr + sr | NA | NA | NA | NA | NA |