HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly

Table 5

Results for HaVec.

File name	k	Hash table index	6 bytes per k-mer runtime (sec)	5 bytes per k-mer runtime (sec)	6 bytes per k-mer total memory (MB)	5 bytes per k-mer total memory (MB)	Unique k-mer in hash table	Unique k-mer in vector	Total unique k-mer
50 m.fa	27	3,558,218,093	2261.75	2163	21445.9392	18052.608	2,358,010,004	14,135,390	2,372,145,394
50 m.fa	32	3,283,745,651	2183	2038.5	19228.8768	16648.4992	2,176,128,060	13,035,689	2,189,163,749
Ecoli_MG1655_s_6_1_bfast.fasta	27	20,115,587	70.25	70	144.896	125.7472	13,330,622	79,768	13,410,390
Ecoli_MG1655_s_6_1_bfast.fasta	32	20,693,341	69.375	68.75	148.3776	128.6144	13,713,606	81,955	13,795,561
Ecoli_MG1655_s_6_2_bfast.fasta	27	196,614,919	488.5	486.5	1205.8624	1018.368	130,293,923	782,686	131,076,609
Ecoli_MG1655_s_6_2_bfast.fasta	32	200,937,899	480.75	476.5	1231.872	1040.2816	133,158,739	799,832	133,958,571
Human1_95G_CASAVA1.8a2_NCBI37_18Jan11_chr19.sorted.fasta	27	313,251,713	601.5	593.25	1909.0432	1610.24	207,579,166	1,255,278	208,834,444
Human1_95G_CASAVA1.8a2_NCBI37_18Jan11_chr19.sorted.fasta	32	334,345,241	611.625	592.75	2035.6096	1716.736	221,565,835	1,330,984	222,896,819
Human1_95G_CASAVA1.8a2_NCBI37_18Jan11_chr21.sorted.fasta	27	199,165,411	371.5	370.625	1221.4272	1031.4752	131,981,455	795,486	132,776,941
Human1_95G_CASAVA1.8a2_NCBI37_18Jan11_chr21.sorted.fasta	32	207,852,223	374.75	374.5	1273.4464	1075.2	137,741,484	826,661	138,568,145
NA19240_GAIIx_100_chr21.fasta	27	163,949,171	508.625	513.5	1009.5616	853.1968	108,643,167	656,266	109,299,433
NA19240_GAIIx_100_chr21.fasta	32	170,662,721	549	504.625	1016.3712	886.9888	113,094,644	680,508	113,775,152
dataset_1_7GB.fa	27	199,165,411	395.25	368.125	1221.4272	1031.4752	131,981,455	795,486	132,776,941
dataset_1_7GB.fa	32	207,852,223	373.75	367	1273.4464	1075.2	137,741,484	826,661	138,568,145
dataset_1_9GB.fa	27	163,949,171	516	507.125	1009.5616	853.1968	108,643,167	656,266	109,299,433
dataset_1_9GB.fa	32	170,662,721	511.375	507.625	1049.8048	886.9888	113,094,644	680,508	113,775,152