Table 1:
Comparison of other tools with LeTRS
| LeTRS | Periscope | SARS-CoV-2–leader | SuPER | ||
|---|---|---|---|---|---|
| Input files | fastq | fastq | bam/sam | sam | |
| Consideration of amplicon primer information used | yes | yes | no | no | |
| Consideration of paired-end Illumina data | yes | no | no | no | |
| Consideration of amplicon primer pool | yes | no | no | no | |
| Consideration of the ACGAAC box | yes | no | no | yes | |
| Support of amplicon Illumina data | yes | yes | yes | yes | |
| Support of amplicon Nanopore data | yes | yes | yes | yes | |
| Support of Nanopore dRNAseq data | yes | no | yes | yes | |
| Method | Fusion site searching | Sequences tag searching | Sequences tag searching | Fusion site searching | |
| Accuracy | ARTIC-Illumina | 1.0000 | 0.9998 | 0.9998 | 0.9996 |
| ARTIC-Nanopore | 0.9985 | 0.9981 | 0.9980 | 0.9979 | |
| Nanopore dRNAseq | 0.9982 | 0.9948 | 0.9937 | ||
| Sensitivity | ARTIC-Illumina | 0.9997 | 0.9498 | 0.9644 | 0.9230 |
| ARTIC-Nanopore | 0.6294 | 0.5326 | 0.5154 | 0.4843 | |
| Nanopore dRNAseq | 0.8448 | 0.5949 | 0.4817 | ||
| Specificity | ARTIC-Illumina | 1.0000 | 1.0000 | 1.0000 | 1.0000 |
| ARTIC-Nanopore | 1.0000 | 1.0000 | 1.0000 | 1.0000 | |
| Nanopore dRNAseq | 1.0000 | 1.0000 | 1.0000 | ||
| F-measure | ARTIC-Illumina | 0.9998 | 0.9499 | 0.9655 | 0.9243 |
| ARTIC-Nanopore | 0.7621 | 0.6699 | 0.6611 | 0.6215 | |
| Nanopore dRNAseq | 0.9157 | 0.7140 | 0.5934 | ||
Accuracy, sensitivity, specificity, and F-measure score were calculated with simulated Illumina and Nanopore sequencing reads for the known subgenomic mRNAs.