Final results for the comparison of the polishing of uncorrected P. falciparum and T. brucei sequences by Pilon and iCORN2
| . | Polishing tool (5 iterations) . | No. of annotated pseudogenes . | Runtime (hours) . |
|---|---|---|---|
| P. falciparum | (None, uncorrected) | 520 | – |
| (None, reference) | 158 | – | |
| Pilon | 210 | 1.91 | |
| iCORN2 | 143 | 9.04 | |
| T. brucei | (None, uncorrected) | 5346 | – |
| (None, reference) | 4925 | – | |
| Pilon | 5037 | 22.51 | |
| iCORN2 | 5179 | 19.35 |
| . | Polishing tool (5 iterations) . | No. of annotated pseudogenes . | Runtime (hours) . |
|---|---|---|---|
| P. falciparum | (None, uncorrected) | 520 | – |
| (None, reference) | 158 | – | |
| Pilon | 210 | 1.91 | |
| iCORN2 | 143 | 9.04 | |
| T. brucei | (None, uncorrected) | 5346 | – |
| (None, reference) | 4925 | – | |
| Pilon | 5037 | 22.51 | |
| iCORN2 | 5179 | 19.35 |
The Bowtie2 aligner to map Illumina short reads (100 bp in the case of P. falciparum) and 5 iterations in both iCORN2 and Pilon were used. The number of annotated pseudogenes by Companion in the pre-polished sequences is included as reference. We compared the number of annotated pseudogenes for each correction and organism. The number of pseudogenes in T. brucei may be due to the presence of large numbers of incomplete copies of variant surface genes. Supplementary Tables 2 and 3 provide detailed information.
Final results for the comparison of the polishing of uncorrected P. falciparum and T. brucei sequences by Pilon and iCORN2
| . | Polishing tool (5 iterations) . | No. of annotated pseudogenes . | Runtime (hours) . |
|---|---|---|---|
| P. falciparum | (None, uncorrected) | 520 | – |
| (None, reference) | 158 | – | |
| Pilon | 210 | 1.91 | |
| iCORN2 | 143 | 9.04 | |
| T. brucei | (None, uncorrected) | 5346 | – |
| (None, reference) | 4925 | – | |
| Pilon | 5037 | 22.51 | |
| iCORN2 | 5179 | 19.35 |
| . | Polishing tool (5 iterations) . | No. of annotated pseudogenes . | Runtime (hours) . |
|---|---|---|---|
| P. falciparum | (None, uncorrected) | 520 | – |
| (None, reference) | 158 | – | |
| Pilon | 210 | 1.91 | |
| iCORN2 | 143 | 9.04 | |
| T. brucei | (None, uncorrected) | 5346 | – |
| (None, reference) | 4925 | – | |
| Pilon | 5037 | 22.51 | |
| iCORN2 | 5179 | 19.35 |
The Bowtie2 aligner to map Illumina short reads (100 bp in the case of P. falciparum) and 5 iterations in both iCORN2 and Pilon were used. The number of annotated pseudogenes by Companion in the pre-polished sequences is included as reference. We compared the number of annotated pseudogenes for each correction and organism. The number of pseudogenes in T. brucei may be due to the presence of large numbers of incomplete copies of variant surface genes. Supplementary Tables 2 and 3 provide detailed information.
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