Table 1.
Detailed HoCoRT performance on simulated human gut microbiome datasets
| Pipeline | Runtime | Accuracy | Precision | Sensitivity |
|---|---|---|---|---|
| Paired-end HiSeq | ||||
| Seal | 291.3 | 0.9975 | 0.8027 | 1.0000 |
| BBDuk | 233.7 | 0.9952 | 0.6786 | 1.0000 |
| BBSplit | 509.0 | 0.9982 | 0.8523 | 1.0000 |
| BioBloom | 66.6 | 0.9990 | 0.9143 | 0.9995 |
| Bowtie2_end-to-end | 77.4 | 0.9988 | 0.8978 | 1.0000 |
| Bowtie2_local | 80.4 | 0.9978 | 0.8187 | 1.0000 |
| Bowtie2_end-to-end_un_conc | 277.2 | 0.9934 | 0.9351 | 0.3625 |
| Bowtie2_local_un_conc | 314.9 | 0.9941 | 0.8956 | 0.4614 |
| HISAT2 | 101.7 | 0.9990 | 0.9145 | 0.9998 |
| Kraken2 | 49.8 | 0.9980 | 0.8385 | 0.9928 |
| BBMap_default | 1053.2 | 0.9982 | 0.8520 | 1.0000 |
| BBMap_fast | 300.9 | 0.9986 | 0.8762 | 0.9999 |
| BWA_MEM2 | 381.3 | 0.9720 | 0.2635 | 1.0000 |
| Kraken2Bowtie2 | 87.7 | 0.9980 | 0.8385 | 1.0000 |
| Kraken2HISAT2 | 117.2 | 0.9980 | 0.8388 | 1.0000 |
| Minimap2_illumina | 73.3 | 0.9977 | 0.8170 | 1.0000 |
| Kraken2Minimap2_illumina | 105.2 | 0.9976 | 0.8107 | 1.0000 |
| Paired-end MiSeq | ||||
| Seal | 376.7 | 0.9967 | 0.7559 | 1.0000 |
| BBDuk | 299.7 | 0.9916 | 0.5457 | 1.0000 |
| BBSplit | 791.9 | 0.9985 | 0.8726 | 1.0000 |
| BioBloom | 142.0 | 0.9990 | 0.9129 | 0.9969 |
| Bowtie2_end-to-end | 159.0 | 0.9989 | 0.9041 | 0.9999 |
| Bowtie2_local | 249.8 | 0.9975 | 0.8043 | 1.0000 |
| Bowtie2_end-to-end_un_conc | 747.3 | 0.9904 | 0.9721 | 0.0457 |
| Bowtie2_local_un_conc | 810.6 | 0.9919 | 0.8761 | 0.2243 |
| HISAT2 | 212.6 | 0.9990 | 0.9224 | 0.9901 |
| Kraken2 | 99.0 | 0.9973 | 0.7902 | 0.9960 |
| BBMap_default | 2338.7 | 0.9985 | 0.8730 | 0.9993 |
| BBMap_fast | 733.3 | 0.9989 | 0.9044 | 0.9956 |
| BWA_MEM2 | 2889.4 | 0.9128 | 0.1032 | 1.0000 |
| Kraken2Bowtie2 | 189.2 | 0.9973 | 0.7908 | 1.0000 |
| Kraken2HISAT2 | 236.2 | 0.9973 | 0.7908 | 1.0000 |
| Minimap2_illumina | 136.5 | 0.9970 | 0.7698 | 1.0000 |
| Kraken2Minimap2_illumina | 170.9 | 0.9967 | 0.7567 | 1.0000 |
| Single-end Nanopore | ||||
| BioBloom | 171.6 | 0.9900 | 1.0000 | 0.0013 |
| Minimap2_nanopore | 179.7 | 0.9950 | 0.9965 | 0.5027 |
| Kraken2Minimap2_nanopore | 256.3 | 0.9957 | 0.9632 | 0.5916 |
| Kraken2 | 162.4 | 0.9938 | 0.9491 | 0.3994 |
The average runtime (in seconds), accuracy, precision, and sensitivity are shown for each pipeline and for each data type. The best (bold) and worst (italic) performing pipelines are indicated for each performance metric and data type