Table 2.
Assembly pipelines and descriptive statistics of PDB70 amplicon reads obtained with Illumina and MinION nanopore
| Pipeline | Type | Input | Error corrector | Contig assembler | Consensus size (bp) | GC% | Coveragea | Identity between chamois and Ovis aries DRB (GenBank AM884914) |
|---|---|---|---|---|---|---|---|---|
| CANU | De novo | MinION | Pilon | CANU | 9001 | 40.86 | ×7139.92 | 95.81% |
| Geneious | De novo | MinION | Pilon | Geneious algorithm | 9048 | 40.86 | ×7120.34 | 95.81% |
| DBG2OLC | Hybrid | Illumina, MinION | Pilon | Velvet (short reads) | 8931 | 40.87 | ×7065.76 | 91.75% |
aThe coverage was calculated using Samtools (Li et al. 2009) considering Illumina reads mapped to Pilon-polished CANU, Geneious and DBG2OLC assemblies, respectively