Table 1 Percent concordance by gene for 31 development batch samples aligned via BWA-MEM aligner and Minimap2 aligner
From: A computational HLA allele-typing protocol to de-noise and leverage nanopore amplicon data
| Â | BWA Aligner | Minimap2 Aligner | ||||
|---|---|---|---|---|---|---|
Gene | 1st field | 2nd field | 3rd field | 1st field | 2nd field | 3rd field |
(% success) | (% success) | (% success) | (% success) | (% success) | (% success) | |
HLA-A | 98.4% | 98.4% | 98.4% | 100.0% | 98.4% | 98.4% |
HLA-B | 100.0% | 96.8% | 96.8% | 98.4% | 93.5% | 93.5% |
HLA-C | 100.0% | 98.4% | 98.4% | 100.0% | 98.4% | 98.4% |
HLA-DPA1 | 100.0% | 96.8% | 96.8% | 100.0% | 98.4% | 93.5% |
HLA-DPB1 | 100.0% | 100.0% | 98.4% | 98.4% | 98.4% | 98.4% |
HLA-DQA1 | 100.0% | 98.4% | 98.4% | 91.9% | 77.4% | 77.4% |
HLA-DQB1 | 100.0% | 98.4% | 98.4% | 100.0% | 98.4% | 98.4% |
HLA-DRB1 | 83.9% | 64.5% | 64.5% | 83.9% | 66.1% | 66.1% |
HLA-DRB3 | 82.6% | 73.9% | 73.9% | 82.6% | 73.9% | 73.9% |
HLA-DRB4 | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 93.8% |
HLA-DRB5 | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% | 100.0% |
Overall | 97.2% | 93.4% | 93.2% | 96.1% | 90.8% | 90.1% |