Table 1.
Assembly pipeline and software usage. Software citations are listed in the text
| Assembly | Software | Version |
|---|---|---|
| Filtering PacBio HiFi adapters | HiFiAdapterFilt https://github.com/sheinasim/HiFiAdapterFilt |
Commit 64d1c7b |
| K-mer counting | Meryl | 1 |
| Estimation of genome size and heterozygosity | GenomeScope | 2 |
| De novo assembly (contiging) | HiFiasm | 0.16.1-r375 |
| Long-read, genome–genome alignment | minimap2 | 2.16 |
| Remove low-coverage, duplicated contigs | purge_dups | 1.2.6 |
| Scaffolding | ||
| Omni-C mapping for SALSA | Arima Genomics mapping pipeline https://github.com/ArimaGenomics/mapping_pipeline |
Commit 2e74ea4 |
| Omni-C Scaffolding | SALSA | 2 |
| Gap closing | YAGCloser https://github.com/merlyescalona/yagcloser |
Commit 20e2769 |
| Omni-C Contact map generation | ||
| Short-read alignment | bwa | 0.7.17-r1188 |
| SAM/BAM processing | samtools | 1.11 |
| SAM/BAM filtering | pairtools | 0.3.0 |
| Pairs indexing | pairix | 0.3.7 |
| Matrix generation | Cooler | 0.8.10 |
| Matrix balancing | hicExplorer | 3.6 |
| Contact map visualization | HiGlass | 2.1.11 |
| PretextMap | 0.1.4 | |
| PretextView | 0.1.5 | |
| PretextSnapshot | 0.0.3 | |
| Organelle assembly | ||
| Mitogenome assembly | MitoHiFi | 2 Commit c06ed3e |
| Genome quality assessment | ||
| Basic assembly metrics | QUAST | 5.0.2 |
| Assembly completeness | BUSCO | 5.0.0 |
| Merqury | 1 | |
| Contamination screening | ||
| Local alignment tool | BLAST+ | 2.10 |
| General contamination screening | BlobToolKit | 2.3.3 |