TABLE 2.
Identifying and comparing errors in HMT-348-TM7c-JB assembliesa
| Assembly | % identity | No. of mismatches |
|---|---|---|
| 16S rRNA sequence % identity to HMT-348 16S rRNA on HOMD | ||
| Polypolish | 99.77% | 3 |
| Illumina-spades | 96.84% | 41 |
| Medaka | 99.92% | 1 |
| Pilon | 98.23% | 23 |
| Unicycler | 98.15% | 24 |
| Flye | 99.92% | 1 |
| Trycycler | 99.92% | 1 |
| Assembly | No. missing or truncated ORFs | Notes |
| Broken ORFs | ||
| Polypolish | 3 | only missing small hypothetical proteins |
| Illumina-spades | 53 | 1 large region that was missing accounted for ~35 |
| Medaka | 137 | |
| Pilon | 5 | only 2 are the same |
| Unicycler | 5 | |
| Flye | 189 | |
| Trycycler | 124 | |
| Assembly | CDSs | Length |
| No. of CDSs | ||
| Polypolish | 804 | 841,260 |
| Illumina-spades | 774 | 788,149 |
| Medaka | 1,008 | 841,361 |
| Pilon | 807 | 841,266 |
| Unicycler | 807 | 841,180 |
| Flye | 1,102 | 841,704 |
| Trycycler | 1,021 | 841,085 |
a
HOMD, Human Oral Microbiome Database; ORFs, open reading frames; CDSs, coding DNA sequences.