Table 4. Timing and memory usage to align PacBio and Illumina reads to the Arabidopsis thaliana reference genome.
Timings reported here include the time used to build the genome index. The alignments reported by nucmer3 and nucmer4 for the Illumina data were identical. Nucmer3 experienced a reproducible crash when aligning PacBio reads to the A. thaliana reference.
| PacBio | Illumina | |||||||
|---|---|---|---|---|---|---|---|---|
| time (min) | memory (MB) | aligned (Mbp) | aligned reads | time (min) | memory (MB) | aligned (Mbp) | aligned reads | |
| blasr | 95 | 4065 | 1780 | 435888 | ||||
| bwa-mem | 49 | 2162 | 1944 | 420912 | 30 | 3360 | 6112 | 21874366 |
| bowtie2 | 24 | 686 | 5580 | 18716070 | ||||
| nucmer3 | fail | fail | fail | fail | 334 | 4688 | 5651 | 19873013 |
| nucmer4 | 24 | 5743 | 1713 | 424271 | 29 | 1283 | 5651 | 19873013 |