Table 2 Preliminary assemblies using five assembly strategies
Metrics | Allpaths | Allpaths+PBJelly | Allpaths+SSPACE-longread | SPAdes | Falcon |
|---|---|---|---|---|---|
Libraries | Paired-end Mate-pair | Paired-end Mate-pair PacBio | Paired-endMate-pair PacBio | Paired-end Mate-pair PacBio | PacBio |
Number of scaffolds | 340 | 235 | 150 | 199 | 59 |
Number of contigs | 1000 | 278 | 1018 | 261 | 59 |
Assembly size (Mbp) | 41.6 | 42.7 | 42.3 | 42.1 | 42.2 |
N50 value (scaffolds) | 628.3 kbp | 764.8 kbp | 947.1 kbp | 1.1 Mbp | 1.6 Mbp |
N50 value (contigs) | 152.4 kbp | 621.3 kbp | 149.5 kbp | 766.3 kbp | 1.6 Mbp |
Number of scaffolds > 1 Mbp (scaffold sizes sum) | 5 (8.4 Mbp) | 7 (12.9 Mbp) | 11 (18.6 Mbp) | 12 (22.8 Mbp) | 15 (29.2 Mbp) |
Complete BUSCOs | 1298 | 1304 | 1300 | 1301 | 1298 |
Fragmented BUSCOs | 24 | 20 | 22 | 21 | 22 |
Missing BUSCOs | 13 | 11 | 13 | 13 | 15 |
CGAL value | −3.61e + 09 | −3.52e + 09 | −3.90e + 09 | −1.12e + 09 | −2.83e + 09 |