GAM-NGS: genomic assemblies merger for next generation sequencing

BMC Bioinformatics

Table 5 GAGE statistics (contiguity, duplication and compression) on Rhodobacter sphaeroides.

Assembler	Ctg num	NG50 (kb)	NG50 corr. (kb)	Assembly size (%)	Chaff size (%)	Unaligned ref (%)	Unaligned asm (%)	Dupl (%)	Comp (%)
Allpaths-LG	204	42.45	34.42	99.68	0.01	0.45	0.01	0.38	0.31
MSR-CA	395	22.12	19.08	97.02	0.01	3.47	0.04	1.05	0.53
Allpaths-LG + MSR-CA
GAM-NGS	168	51.12	37.88	99.97	0.00	0.28	0.01	0.61	0.31
GAA	164	53.82	40.55	100.07	0.01	0.20	0.01	0.63	0.32
ZORRO	216	38.87	30.64	100.41	0.03	0.36	0.02	0.43	0.48
MSR-CA + Allpaths-LG
GAM-NGS	199	49.61	37.88	97.95	0.01	3.10	0.04	1.58	0.61
GAA	177	54.71	40.55	99.74	0.01	1.61	0.04	1.08	0.35
ZORRO	206	44.61	38.79	101.14	0.09	0.21	0.06	1.64	0.25
Bambus2	177	93.19	12.78	94.97	0.00	4.92	0.01	0.00	0.24
SOAPdenovo	202	131.68	14.34	100.29	0.44	0.76	0.01	1.30	0.46
Bambus2 + SOAPdenovo
GAM-NGS	83	149.75	14.16	98.32	0.00	3.02	0.00	1.59	0.63
GAA	100	194.16	14.74	98.35	0.13	2.28	0.01	0.63	0.58
ZORRO	711	16.56	13.18	100.48	0.89	0.66	0.25	1.05	0.59
SOAPdenovo + Bambus2
GAM-NGS	177	154.47	15.17	100.41	0.42	0.82	0.01	1.67	0.48
GAA	174	188.18	14.54	100.35	0.44	0.76	0.01	1.38	0.48
ZORRO	720	16.56	12.78	100.48	0.84	0.69	0.24	1.14	0.56

For each assembler we report the number of contigs greater than 200 bp (Ctg), the NG50, the corrected NG50 (NG50 computed breaking the assembly at each error), assembly's total length, the percentage of short (Chaff) contigs, the length of reference's regions which cannot be found in the assembly (Unaligned ref), the length of assembly's regions that cannot be found in the reference (Unaligned asm), the percentage of duplicated (Dupl) and compressed (Comp) regions in the assembly. All the percentages in the table are computed with respect to the true genome size.

ISSN: 1471-2105