Table 2.
Summary of scaffolding performance of AGOUTI and RNAPATH with K = 2
| Assembly | Program | No. of contigs scaffolded | No. of scaffolds in final assembly | Scaffold N50 | No. of gene models in final assembly |
|---|---|---|---|---|---|
| CE1 | AGOUTI | 5,349 | 8,525 | 36,096 | 21,776 |
| RNAPATH | 3,421 | 9,841 | 28,769 | - | |
| RNAPATHD | 5,323 | 8,528 | 36,235 | - | |
| CE2 | AGOUTI | 3,879 | 5,974 | 73,881 | 20,951 |
| RNAPATH | 2,430 | 6,933 | 58,959 | - | |
| RNAPATHD | 3,869 | 5,976 | 73,770 | - | |
| CE3 | AGOUTI | 3,093 | 5,243 | 97,924 | 20,658 |
| RNAPATH | 1,980 | 5,968 | 85,802 | - | |
| RNAPATHD | 3,082 | 5,244 | 100,700 | - | |
| CE4 | AGOUTI | 2,678 | 4,242 | 127,283 | 20,324 |
| RNAPATH | 1,618 | 4,937 | 103,844 | - | |
| RNAPATHD | 2,671 | 4,242 | 127,283 | - | |
| CE5 | AGOUTI | 1,966 | 3,284 | 258,507 | 19,978 |
| RNAPATH | 1,225 | 3,760 | 202,360 | - | |
| RNAPATHD | 1,961 | 3,285 | 258,507 | - | |
| CE6 | AGOUTI | 941 | 1,501 | 642,283 | 19,411 |
| RNAPATH | 511 | 1,774 | 492,192 | - | |
| RNAPATHD | 934 | 1,504 | 642,283 | - | |
| AGOUTI | 1,358 | 5,743 | 73,952 | 23,666 | |
| N2/CB | RNAPATH | 762 | 6,118 | 65,196 | - |
| RNAPATHD | 1,376 | 5,722 | 74,347 | - | |
| AGOUTI | 20,594 | 89,452 | 27,524 | 79,222 | |
| Lyco | RNAPATH | 8,797 | 97,181 | 24,127 | - |
| RNAPATHD | 20,529 | 89,301 | 28,202 | - |
DRNAPATH run with denoised joining-pairs. Best-performing programs are highlighted in bold