Table 2. Comparison of various mappers for structural variant calling.
| LAST | marginAlign | BWA-MEM | BLASR | DALIGNER | GraphMap | |
|---|---|---|---|---|---|---|
| Precision (%) | 0 | 50 | 67 (90) | 94 | 0 | 100 |
| Recall (%) | 0 | 5 | 10 (45) | 75 | 0 | 100 |
| F1 score (%) | 0 | 9 | 17 (60) | 83 | 0 | 100 |
Results are based on mapping a MinION data set for E. coli K-12 (R7.3) on a mutated reference containing insertion and deletions in a range of sizes ((100 bp, 300 bp, 500 bp, 1 kbp, 1.5 kbp, 2 kbp, 2.5 kbp, 3 kbp, 3.5 kbp and 4 kbp); 20 events in total). Bold values indicate the best results for each metric. The F1 score is given by a weighted average of precision and recall. Values in parentheses for BWA-MEM show the results using LUMPY.