BASE: a practical de novo assembler for large genomes using long NGS reads

BMC Genomics

Table 4 Mismatches analysis for human genome assembly

Dataset	Assembler	Whole genome mismatches				Exon region mismatches
Dataset	Assembler	Total	Variant Call	Public SNP	Novel	Total	Variant Call	Public SNP	Novel
YH_100bp	SOAPdenovo2	2,735,141	2,423,482	108,044	203,615	47,926	40,701	1,590	5,635
YH_100bp	BASE	3,479,046	2,872,396	208,351	398,299	47,515	42,124	1,724	3,667
YH_150bp	SOAPdenovo2	2,911,990	2,613,670	113,037	185,283	46,002	43,151	1,148	1,703
YH_150bp	BASE	3,839,110	3,075,913	256,217	506,980	52,561	46,420	1,822	4,319
NA12878_150bp	SOAPdenovo2	2,301,111	2,025,220	109,497	166,394	39,702	35,644	1,740	2,318
NA12878_150bp	BASE	3,459,648	3,052,269	129,933	277,446	49,711	45,361	1,151	3,199
NA12878_250bp	SOAPdenovo2	2,544,785	2,122,144	130,806	291,835	42,744	35,890	1,936	4,918
NA12878_250bp	BASE	3,751,887	2,613,065	604,805	534,017	48,635	37,853	5,068	5,714

We mapped the assembled contigs to Hg19 and got the mismatches between each contig and reference sequence. Then we used the detected SNPs and SNPs from published SNP databases to analysis these mismatches in whole genome and exon regions respecitively

ISSN: 1471-2164