Table 1.
Assembly pipeline and software used.
| Assembly | Software | Version |
|---|---|---|
| Kmer counting | Jellyfish | 2.2.6 |
| Estimation of genome size and heterozygosity | GenomeScope | 2 |
| De novo assembly (contigging) | ipa | 1.3.1 |
| Long read, genome–genome alignment | Minimap2 | 2.22 |
| Scaffolding | ||
| HiC mapping | Phase Genomics Proximo HiC pipeline https://phasegenomics.github.io/2019/09/19/hic-alignment-and-qc.html |
Commit 5f9d55ea3162f8d21988f486b5d012f0800abdc4 |
| HiC scaffolding | Juicebox | 2 |
| HiC contact map generation | ||
| Short-read alignment | BWA-MEM | 0.7.17-r1188 |
| SAM/BAM processing | SAMBLASTER | 1.11 |
| SAM/BAM filtering | samtools | 0.3.0 |
| Matrix generation and balancing | Phase Genomics Proximo HiC Pipeline | Commit 5f9d55ea3162f8d21988f486b5d012f0800abdc4 |
| Benchmarking | ||
| Basic assembly stats | QUAST | 5.0.2 |
| GenomeTools | 1.5.9 | |
| Assembly completeness | BUSCO | 5.2.2 |
| Merqury | 1.3 | |
| Blobtoolkit | 3.1.6 | |
| Repeat analysis | RepeatModeler | 1.0.11 |
| RepeatMasker | 4.1.2 | |
| Gene prediction | Augustus | 3.3.3 |
Software citations are listed in the text.