Table 1.
Assembly pipeline and software used.
| Assembly | Software and options | Version |
|---|---|---|
| Filtering PacBio HiFi adapters | HiFiAdapterFilt | Commit 64d1c7b |
| K-mer counting | Meryl (k = 21) | 1 |
| Estimation of genome size and heterozygosity | GenomeScope | 2 |
| De novo assembly (contiging) | HiFiasm (Hi-C Mode, –primary, output p_ctg.hap1, p_ctg.hap2) | 0.16.1-r375 |
| Remove low-coverage, duplicated contigs | purge_dups | 1.2.6 |
| Scaffolding | ||
| Omni-C scaffolding | SALSA (-DNASE, -i 20, -p yes) | 2 |
| Gap closing | YAGCloser (-mins 2 -f 20 -mcc 2 -prt 0.25 -eft 0.2 -pld 0.2) | Commit 0e34c3b |
| Omni-C contact map generation | ||
| Short-read alignment | BWA-MEM (-5SP) | 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 (hicCorrectmatrix correct --filterThreshold -2 4) | 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 (-r, -p 50, -o 1) | 2 Commit c06ed3e |
| Genome quality assessment | ||
| Basic assembly metrics | QUAST (--est-ref-size) | 5.0.2 |
| Assembly completeness | BUSCO (-m geno, -l tetrapoda) | 5.0.0 |
| Merqury | 2020-01-29 | |
| Contamination screening | ||
| Local alignment tool | BLAST+ | 2.1 |
| General contamination screening | BlobToolKit | 2.3.3 |
Software citations are listed in the text.