Readjoiner: a fast and memory efficient string graph-based sequence assembler

BMC Bioinformatics

Table 1 Comparison of Readjoiner and Edena

	RJ	Edena	$\frac{Edena}{RJ}$	RJ	Edena	$\frac{Edena}{RJ}$	RJ	Edena	$\frac{Edena}{RJ}$
Read set	c22	c22	-	c15	c15	-	c7	c7	-
Genome size (Mbp)	34.9	34.9	-	81.7	81.7	-	155.4	155.4	-
Number of reads (M)	7.0	7.0	-	16.3	16.3	-	31.1	31.1	-
Contained reads (K)	686.4	686.4	-	1665.7	1665.7	-	3103.0	3103.0	-
Irreducible SPM (M)	7.2	7.2	-	17.2	17.2	-	36.4	36.4	-
Overall time (s)	360	4903	13.62×	945	13609	14.40×	2035	29404	14.45×
Overall space (MB)	294	2753	9.35×	703	6415	9.13×	1331	12255	9.21×
Contigs	120712	120462	-	254830	254111	-	503446	502706	-
Total contigs length (Mbp)	45.7	44.7	-	103.0	101.1	-	198.8	195.0	-
Assembly N50 (Kbp)	1.6	1.7	-	2.4	2.5	-	2.3	2.4	-
Assembly NG50 (Kbp)	2.7	2.7	-	3.7	3.7	-	3.9	3.9	-
Longest contig (Kbp)	41.4	41.4	-	54.2	54.2	-	44.9	44.9	-

Results of applying Readjoiner (RJ) and Edena to the datasets c22, c15, c7 (ℓ_min = 45).

ISSN: 1471-2105