Table 4. Software tools: versions and sources.
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.2.1 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| bwa-mem2 | 2.2.1 | https://github.com/bwa-mem2/bwa-mem2 |
| Cooler | 0.8.11 | https://github.com/open2c/cooler |
| Gfastats | 1.3.6 | https://github.com/vgl-hub/gfastats |
| Hifiasm | 0.16.1-r375 | https://github.com/chhylp123/hifiasm |
| HiGlass | 1.11.6 | https://github.com/higlass/higlass |
| Merqury.FK | d00d98157618f4e8d1a9
190026b19b471055b22e |
https://github.com/thegenemyers/MERQURY.FK |
| MitoHiFi | 2 | https://github.com/marcelauliano/MitoHiFi |
| PretextView | 0.2 | https://github.com/wtsi-hpag/PretextView |
| purge_dups | 1.2.3 | https://github.com/dfguan/purge_dups |
| sanger-tol/
genomenote |
v1.0 | https://github.com/sanger-tol/genomenote |
| sanger-tol/
readmapping |
1.1.0 | https://github.com/sanger-tol/readmapping/tree/1.1.0 |
| Singularity | 3.9.0 | https://github.com/sylabs/singularity |
| YaHS | 1.2a | https://github.com/c-zhou/yahs |