Wrapper to generate phased assemblies with PacBio HiFi + Hi-C reads.
| Parameter | Description |
|---|---|
| --hifi_reads | Path to PacBio HiFi reads |
| --hic_reads | Path to Hi-C reads |
| --species_id | Name for the species, used in generating Hifiasm assembly |
| --nthreads | Number of threads to use. Default is 16 |
| --est_ref_size | Default is 800000000 (800Mb). for Quast's NG50 |
- Hifiasm: https://github.com/chhylp123/hifiasm
- YaHS: https://github.com/c-zhou/yahs
- bwa-mem2: https://github.com/bwa-mem2/bwa-mem2
- QUAST: https://github.com/ablab/quast
- BUSCO: https://gitlab.com/ezlab/busco