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

BMC Bioinformatics

Table 2 Comparison of Readjoiner and SGA

	RJ	SGA	$\frac{SGA}{RJ}$	RJ	SGA	$\frac{SGA}{RJ}$	RJ	SGA	$\frac{SGA}{RJ}$	RJ	SGA	$\frac{SGA}{RJ}$
Read set	c22	c22	-	c15	c15	-	c7	c7	-	c2	c2	-
Genome size (Mbp)	34.9	34.9	-	81.7	81.7	-	155.4	155.4	-	238.2	238.2	-
Number of reads (M)	7.0	7.0	-	16.3	16.3	-	31.1	31.1	-	47.6	47.6	-
Sga index -d (K)	-	300	-	-	700	-	-	1350	-	-	2300	-
Overall time (s)	360	7508	20.86×	945	19334	20.46×	2035	39988	19.65×	3185	65194	20.47×
Overall space (MB)	294	383	1.30×	703	842	1.20×	1331	1568	1.18×	2094	2436	1.16×
Contigs	120712	231594	-	254830	547217	-	503446	1215816	-	634403	1702714	-
Total contigs length (Mbp)	45.7	55.9	-	103.0	130.5	-	198.8	266.4	-	292.2	396.1	-
Assembly N50 (Kbp)	1.6	0.8	-	2.4	1.0	-	2.3	0.5	-	3.2	1.2	-
Assembly NG50 (Kbp)	2.7	2.7	-	3.7	3.7	-	3.9	3.9	-	4.5	4.5	-
Longest contig (Kbp)	41.4	41.4	-	54.2	54.2	-	44.9	44.9	-	52.9	52.9	-

Results of applying Readjoiner (RJ) and SGA to the datasets c22, c15, c7, c2 (ℓ_min = 45).

ISSN: 1471-2105