Clover: a clustering-oriented de novo assembler for Illumina sequences

Hsieh, Ming-Feng; Lu, Chin Lung; Tang, Chuan Yi

doi:10.1186/s12859-020-03788-9

BMC Bioinformatics

Table 2 Comparison of assemblers on Staphylococcus aureus (SA), Rhodobacter sphaeroides (RS) and human chromosome 14 (HG)

From: Clover: a clustering-oriented de novo assembler for Illumina sequences

Data (Mb	Assembler	Contigs						Scaffolds
Data (Mb	Assembler	Num	N50 (kb)	E-size (kb)	Errs	N50C (kb)	E-sizeC (kb)	Num	N50 (kb)	E-size (kb)	Errs	N50C (kb)	E-sizeC (kb)
SA	Clover	128	43.9	53.1	13	41.3	50.5	12	1490	947	2	1490	890
2.9	ABySS	90	129.1	181.1	16	69.8	102.5	61	170	199	0	107	127
	Bambus2	109	50.2	69.1	178	16.7	19.5	17	1084	1120	0	1084	1120
	CABOG	Could not run because of incompatible read lengths in one library
	MSR-CA	94	59.2	60.4	22	49.2	51.4	17	2412	2026	1	1022	1039
	SGA	1252	4.0	4.7	3	4.0	4.7	546	208	166	2	208	164
	SOAPdenovo	107	288.2	252.3	58	62.7	67.5	99	332	302	0	288	227
	SPAdes	98	62.6	87.9	9	57.0	75.1	41	1703	1144	2	684	570
	Velvet	162	48.4	60.3	19	41.5	49.8	45	762	664	18	284	282
RS	Clover	453	20.1	23.8	19	19.5	21.9	59	2483	1795	1	2483	1795
4.6	ABySS	644	19.7	25.1	57	13.3	18.5	414	51	56	0	46	47
	Bambus2	177	93.2	94.5	360	12.8	16.3	92	2439	1375	1	390	1106
	CABOG	322	20.2	24.1	31	17.9	21.5	130	66	520	3	65	381
	MSR-CA	395	22.1	24.2	32	19.1	21.5	43	2976	2039	3	2976	2017
	SGA	3067	2.3	3.3	4	2.3	3.3	2096	51	53	0	51	53
	SOAPdenovo	204	131.7	157.2	401	14.6	18.7	166	660	688	0	660	559
	SPAdes	768	11.8	13.7	7	11.7	13.5	352	718	840	0	718	840
	Velvet	583	15.7	18.6	24	14.5	16.9	178	353	380	16	301	352
HG	Clover	24,527	3.4	5.3	718	3.2	5.0	2089	839	943	385	409	502
88.3	ABySS	21,222	14.7	19.0	1876	10.4	13.4	19,249	18	24	13	13	19
	Bambus2	13,592	5.9	23.3	8175	4.3	6.3	1792	324	528	240	200	274
	CABOG	3361	45.3	58.8	2346	23.7	30.6	479	393	549	39	309	457
	MSR-CA	30,103	4.9	6.8	1656	4.3	5.9	1425	893	1420	1430	282	407
	SGA	56,939	2.7	3.8	375	2.7	3.7	30,975	83	113	24	81	111
	SOAPdenovo	21,818	16.7	21.9	6587	7.8	10.4	13,502	454	533	384	227	276
	SPAdes	16,854	12.7	16.7	1519	10.4	13.6	9245	173	223	199	129	162
	Velvet	45,564	2.3	3.3	3665	2.1	3.0	3565	1190	1825	8659	86	124

Num the number of sequences produced, N50 the N50 statistic calculated with respect to the genome size, E-size the most likely size of the sequence containing some random base in the genome, Errs the number of misjoins and for the contig value, also the number of indels > 5 bases, N50C the N50 calculated after splitting all sequences at error locations, and E-sizeC the E-size calculated after splitting all sequences at error locations. The best result in each column, for each dataset, is indicated in bold

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