ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

Table 5 ALLPATHS, Velvet and EULER assemblies of five microbial genomes: base accuracy, misassemblies, and long-range validity

	ALLPATHS	Velvet	EULER
Base accuracy
Quality, from class I to III chunks
S. aureus	Q59	Q33	Q32
E. coli	Q67	Q34	Q30
R. sphaeroides	>Q60	Q35	Q29
S. pombe	Q42	Q37	Q29
N. crassa	Q39	Q32	Q28
Misassemblies
% in class IV to V chunks
S. aureus	0.0%	6.6%	8.2%
E. coli	0.0%	6.9%	7.0%
R. sphaeroides	0.3%	3.0%	4.7%
S. pombe	0.5%	3.4%	7.2%
N. crassa	2.2%	13.6%	23.2%
Long-range validity
At 100-kb distance
S. aureus	100.0%	45.6%	99.8%
E. coli	100.0%	86.4%	N/A
R. sphaeroides	100.0%	75.8%	N/A
S. pombe	99.8%	80.2%	100.0%
N. crassa	99.8%	13.6%	N/A

For five genomes, statistics from ALLPATHS, Velvet, and EULER assemblies are shown. Base accuracy: the inferred quality score for the bases in chunk classes I to III, obtained by dividing the number of errors in these chunks by the total number of bases, and then taking -10*log₁₀ of this quantity. Misassemblies: total fraction of bases in chunks in classes IV to V. Long-range validity: we chose 10,000 pairs of 100-base sequences at random from the scaffolds, where the two sequences were separated by 100,000 bases, considering only cases where both sequences could be placed uniquely on the reference. We scored the placement as 'valid' if both sequences were placed on the same chromosome, in the same orientation, with separation 100,000 ± 25% bases. We report the fraction of valid placements. N/A: all scaffolds were of length <100 kb.

ISSN: 1474-760X