TIGER: tiled iterative genome assembler

BMC Bioinformatics

Table 2 The human chromosome 14 assembly results in terms of continuity, accuracy, and statistics.

Evaluations	Continuity			Accuracy			Statistics
	Contig #	NG50 (kbp)	NG50 corr. (kbp)	SNP	Indels	Misjoins	Asm. (%)	Unaligned ref. (%)	Duplicated ref. (%)
Velvet 61k	28,974	5.2	4.7	82,235	17,755	601	96.69	2.09	0.43
Tiger-Velvet-R 125i	20,189	11.6	9.3	84,577	21,847	533	97.90	1.98	1.50
Tiger-Velvet-I 7i	21,623	10.9	8.9	84,811	21,470	654	98.43	1.53	1.48
SOAPdenovo 55k	50,094	3.0	3.0	67,956	11,866	36	95.91	3.13	0.28
Tiger-Soap-R 120i	60,134	3.6	3.4	68,881	12,839	185	99.40	3.01	2.79
Tiger-Soap-I 7i	55,173	3.8	3.6	69,215	13,390	205	98.68	2.43	1.46

The columns include the number of contigs, NG50 size and its error-corrected size, the number of single nucleotide polymorphisms (SNPs), the number of indels and misjoins in contigs, total assembly length, genome coverage (100 - Unaligned ref.), and duplications. K-mer 61 and 55 are the best k-mer sizes for Velvet and SOAPdenovo, respectively. "#k" stands for the applied k-mer size. "#i" stands for the iteration number.

ISSN: 1471-2105