GAM-NGS: genomic assemblies merger for next generation sequencing

BMC Bioinformatics

Table 2 GAGE statistics (contiguity, duplication and compression) on Staphylococcus aureus.

Assembler	Ctg num	NG50 (kb)	NG50 corr. (kb)	Assembly size (%)	Chaff size (%)	Unaligned ref (%)	Unaligned asm (%)	Dupl (%)	Comp (%)
Allpaths-LG	60	96.74	66.23	98.88	0.03	0.61	0.01	0.04	1.26
MSR-CA	94	59.15	48.23	98.60	0.01	1.28	0.00	0.71	0.88
Allpaths-LG + MSR-CA
GAM-NGS	44	141.54	75.82	100.49	0.00	0.44	0.01	0.26	0.99
GAA	40	139.48	80.68	99.52	0.03	0.37	0.01	0.32	0.88
ZORRO	81	74.68	62.85	99.70	0.16	0.32	0.04	0.59	0.88
MSR-CA + Allpaths-LG
GAM-NGS	66	90.47	66.44	100.21	0.01	1.01	0.00	2.03	0.89
GAA	53	131.65	64.43	100.66	0.01	0.95	0.00	1.90	0.79
ZORRO	80	74.64	62.85	99.63	0.14	0.32	0.05	0.53	1.11
Allpaths-LG	60	96.74	66.23	98.88	0.03	0.61	0.01	0.04	1.26
SOAPdenovo	107	288.18	62.68	100.55	0.34	0.22	0.02	1.66	1.45
Allpaths-LG + SOAPdenovo
GAM-NGS	56	107.12	69.39	99.52	0.03	0.56	0.01	0.34	1.26
GAA	40	255.66	83.67	108.10	0.06	0.25	0.01	2.78	1.31
ZORRO	104	76.94	65.83	105.59	0.31	0.15	0.10	5.19	1.36
SOAPdenovo + Allpaths-LG
GAM-NGS	93	288.18	62.68	100.92	0.32	0.20	0.02	1.88	1.40
GAA	74	294.96	62.87	101.92	0.34	0.16	0.02	2.62	1.37
ZORRO	107	76.94	62.68	105.63	0.29	0.16	0.09	5.17	1.50

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