GAM-NGS: genomic assemblies merger for next generation sequencing

BMC Bioinformatics

Table 9 GAGE statistics (SNPs, indels and misjoins) on human chromosome 14.

Assembler	SNPs	Indels < 5 bp	Indels ≥ 5 bp	Misjoins	Inv	Reloc
Allpaths-LG	55319	27563	2558	101	44	57
CABOG	81151	28438	2884	149	46	103
Allpaths-LG + CABOG
GAM-NGS	61725	29936	2950	119	32	87
GAA	63835	30151	2990	123	29	94
CABOG + Allpaths
GAM-NGS	79478	29653	3021	154	43	111
GAA	81763	29812	3008	134	31	103

For each assembly we show the number of SNPs, the number of indels shorter than 5 bp and greater (or equal) than 5 bp. The number of misjoins is computed as the sum of inversions (parts of contigs reversed with respect to the reference genome) and relocations (rearrangements moving a contig within/between chromosomes). All the statistics were computed using the same script with the gapped reference genome (107,349,540 bp).

ISSN: 1471-2105