GAM-NGS: genomic assemblies merger for next generation sequencing

BMC Bioinformatics

Table 8 GAGE statistics (contiguity, duplication and compression) on human chromosome 14.

Assembler	Ctg num	NG50 (kb)	NG50 corr. (kb)	Assembly size (%)	Chaff size (%)	Unaligned ref (%)	Unaligned asm (%)	Dupl (%)	Comp (%)
Allpaths-LG	4529	27.96	15.69	78.67	0.02	20.03	0.04	0.23	2.11
CABOG	3361	35.86	18.63	80.34	0.02	19.13	0.07	0.13	1.39
Allpaths-LG + CABOG
GAM-NGS	2235	61.64	21.91	80.94	0.02	19.08	0.10	0.88	1.43
GAA	1989	69.40	23.04	82.08	0.02	18.92	0.09	1.52	1.39
CABOG + Allpaths-LG
GAM-NGS	1979	66.29	23.63	81.00	0.02	19.00	0.06	0.74	1.37
GAA	1903	70.39	23.89	81.89	0.02	18.98	0.07	1.21	1.36

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 statistics were computed using the same script with the gapped reference genome (107,349,540 bp).

ISSN: 1471-2105