Table 1. The set of tools and their index configuration used in performance comparison.
| Category | Method | Version | Index |
|---|---|---|---|
| iMapSplice | iMapSplice-phased | 1.0 Beta | reference genome (hg19) + individual phased SNPs |
| iMapSplice-unphased | 1.0 Beta | reference genome (hg19) + individual unphased SNPs | |
| Ref-based | MapSplice[9] | 3.0 Beta | reference genome (hg19) |
| HISAT2[18] | 2.0.5 | reference genome (hg19) | |
| STAR (2-pass)[10] | 2.5.1 | reference genome (hg19) | |
| Mask-based | MapSplice MASK | 3.0 Beta | reference genome (hg19) + SNP loci masked with Ns |
| HISAT2 MASK | 2.0.5 | reference genome (hg19) + SNP loci masked with Ns | |
| STAR MASK (2-pass) | 2.5.1 | reference genome (hg19) + SNP loci masked with Ns | |
| SNP-aware | HISAT2 SNP | 2.0.5 | reference genome (hg19) + individual unphased SNPs |
| HISAT2 POP | 2.0.5 | reference genome (hg19) + population SNPs | |
| rPGA[14] | 2.0.0 | reference genome (hg19) + two haplotype personal genomes |