Table 1:
Comparison of run time and genome coverage of resulting synteny blocks between SatsumaSynteny2 and halSynteny
| Genome | Assembly N50 (Mb) | Genome coverage (%) | Time required, min | ||
|---|---|---|---|---|---|
| SatsumaSynteny2 | halSynteny | SatsumaSynteny2 | halSynteny | ||
| Strongyloides ratti | 11.7 | 55.6 | 72.5 | 1,232 | 18 (+496) |
| Strongyloides stercoralis | 0.4 | 56.6 | 55.5 | ||
| Caenorhabditis elegans | 17.5 | 20.0 | 92.5 | 547 | 74 (+496) |
| Caenorhabditisbriggsae | 108.4 | 18.7 | 88.3 | ||
Comparison of run time and genome coverage of resulting synteny blocks between SatsumaSynteny2 and halSynteny. The former was run with extra parameter -threads 10. The latter was run with resolution parameters –maxAnchorDistance 1000000 (1 Mb), –minBlockSize 100000 (100 kb) for S. ratti/S. stercoralis, –maxAnchorDistance 1000000 (1Mb), –minBlockSize 1000000 (1 Mb) for C. elegans/C. briggsae. As a preliminary step for application of halSynteny, the whole-genome alignment among all 4 genomes was constructed using Progressive Cactus software, which took 496 minutes. The assemblies of C. elegans and C. briggsaeare of chromosomal level, while there are scaffold-level assemblies for S. rattiand S. stercoralis.