Table 1. Performance of alignment methods.
| HG002 HiFi | HG002 CLR | HG002 ONT | HG002 HiFi hifiasm hap1 | HG002 HiFi hifiasm hap2 | ||
|---|---|---|---|---|---|---|
| lra | runtime | 942m | 7428m | 1528m | 105m | 90m |
| memory | 12.01G | 16.46G | 13.96G | 31.10G | 28.66G | |
| # of mapped reads | 1.84M | 4.95M | 1.37M | 396 | 411 | |
| # of mapped bases | 35.85Gb | 86.82Gb | 25.45Gb | 2.87Gb | 2.98Gb | |
| minimap2 | runtime | 890m | 1973m | 1358m | 100m | 82m |
| memory | 19.04G | 18.49G | 22.88G | 20.95G | 21.90G | |
| # of mapped reads | 1.85M | 5.06M | 1.41M | 492 | 496 | |
| # of mapped bases | 36.20Gb | 87.36Gb | 25.73Gb | 2.92Gb | 3.01Gb | |
| ngmlr | runtime | 5087m | 33047m | 8862m | - | - |
| memory | 13.6G | 14.67G | 17.00G | - | - | |
| # of mapped reads | 1.78M | 4.84M | 2.07M | - | - | |
| # of mapped bases | 34.59Gb | 83.75Gb | 24.22Gb | - | - |
Each dataset was aligned to GRCh37 by all methods with 16 threads, with—indicating a software crash. Total CPU time is reported. The optimal values in each class are given in bold. The HiFi hifiasm assembly is a haplotype-resolved de novo assembly of HG002 using HiFi reads, with haplotype N50 values of 50.55Mb and 42.92Mb.