Table 1. Statistics of the assemblies generated by different assemblers.
| MaSuRCA (Zimin et al. 2013) | SGA (Simpson and Durbin 2010) | Velvet (Zerbino and Birney 2008) | AbySS (Simpson et al. 2009) | CLC (CLC bio 2017) | Ray (Boisvert et al. 2010) | SOAPdenovo (Luo et al. 2012) | ALLPATHS-LG (Gnerre et al. 2011) | SPAdes (Bankevich et al. 2012) | |
|---|---|---|---|---|---|---|---|---|---|
| Span (bp) | 89,577,071 | 61,516,197 | 58,979,055 | 59,511,073 | 59,525,064 | 59,264,893 | 60,512,111 | 59,578,117 | 59,698,979 |
| No. of scaffolds | 6,646 | 5,619 | 786 | 782 | 520 | 147 | 313 | 151 | 203 |
| Longest scaffold | 134,185 | 836,405 | 1,580,233 | 1,581,252 | 2,304,523 | 3,256,501 | 2,993,798 | 3,772,824 | 4,597,891 |
| N50 | 18,584 | 78,455 | 213,759 | 258,755 | 659,741 | 1,269,874 | 1,466,413 | 1,567,404 | 1,573,002 |
| No. N’s | 3,067,902 | 276,207 | 1,238 | 160,214 | 480,962 | 153,992 | 1,918,481 | 492,105 | 17,036 |
| GC content (%) | 44.5 | 44.5 | 44.5 | 44.5 | 44.5 | 44.5 | 44.5 | 44.5 | 44.5 |
| Absolute REAPR scorea | 3.7 | 8.1 | 9.1 | 9.4 | 6.4 | 2.8 | 1.5 | 5.2 | 8.4 |
| ALE scoreb | −2,909 × 106 | −934 × 106 | −482 × 106 | −467 × 106 | −976 × 106 | −1,110 × 106 | −982 × 106 | −978 × 106 | −291 × 106 |
a
REAPR absolute score measures the frequency of error-free bases and contigs, ranging from 0 to 1.
b
ALE score is computed from the logarithm of the probability that the assembly is correct. ALE scores are negative: the closer to zero, the larger is the probability of the assembly of being correct.