Table 1.
Programs used in assembly
| Purpose | Program | Version |
|---|---|---|
| Oxford Nanopore basecalling | Albacore | 2.0.2 |
| Illumina read trimming | SeqPrep2 | 1.1 |
| Illumina read trimming | Trimmomatic | 0.33 |
| De novo assembly | Meraculous-2D | 2.2.4 |
| Scaffolding | HiRise | 2.1.1 |
| Nanopore adapter trimming | Porechop | 0.2.3 |
| Gap-filling | PBJelly | 15.8.24 |
| Short-read polishing | Pilon | 1.22 |
| Duplicate removal | Samtools rmdup | 0.18 |
| Assembly validation | BUSCO | 5.0.0 |
| k-mer based assembly validation | Merqury | 1.1 |
| Masking of repetitive elements | RepeatMasker | 1.332 4.1.1 |
| Identification of repetitive elements | RepeatScout | 1.0.5 |
| Annotation | Augustus | 3.2.2 |
| RNAseq mapping | TopHat2 | 2.1.0 |
| Protein mapping | Exonerate | 2.2.0 |
| Mitochondrial genome assembly | Unicycler | 0.4.4 |
| Long read mapping | Minimap2 | 2.7-r659 |
| Illumina mapping | BWA | 0.7.12 |
| Mitochondrial genome iterative assembly | MIA | 1.0 |
| Mitochondrial assembly | Jalview | 2.11.0 |