Table 1.
General characteristics of existing polishing algorithms. These seven tools were evaluated in our benchmark with the specified parameters
| Reference | Publication date | Version | Read alignment | Integrated aligner | Parameters used in the benchmark | |
|---|---|---|---|---|---|---|
| Hapo-G | This study | - | 0.1 | yes | BWA | -t 36 |
| Apollo | Firtina C. et al. (12) | 2020 | 2.0 | yes | no | -t 36 |
| POLCA | Ziminn AV. et al. (14) | 2020 | 3.4.2 | yes | BWA | -t 36 |
| HyPo | Kundu R. et al. (13) | 2019 | 1.0.3 | yes | no | -s size* -c 180 -t 36 |
| NextPolish | Hu J. et al. (12) | 2019 | 1.3.2 | yes | BWA | task = best parallel_jobs = 6 multithread_jobs = 6 genome_size = auto |
| ntEdit | Warren RL. et al. (11) | 2019 | 1.3.2 | no | NA | -k 40 -t 36 –outbloom –solid ntEdit: -m 1 -t 36 |
| Racon | Vaser R. et al. (15) | 2017 | 1.4.3 | yes | no | -t 36 |
| Pilon | Walker BJ. et al. (9) | 2014 | 1.23 | yes | no | –threads 36 |
*size = 120Mb (Arabidopsis thaliana), 120Mb (Solanum tuberosum), 100 K (synthetic sequence).