Evaluation of short read metagenomic assembly

Charuvaka, Anveshi; Rangwala, Huzefa

doi:10.1186/1471-2164-12-S2-S8

BMC Genomics

Table 1 Contig Alignment Statistics.

From: Evaluation of short read metagenomic assembly

Dataset	K	Total Contigs	Accurate Contigs	% Accurate Contigs	N50	Total Bases	Bases in Accurate Contigs	% Bases in Accurate Contigs
	C	81451	74790	91.82	466	24892639	24163037	97.07
	C-21	67448	66144	98.07	447	21509228	21300001	99.03
	21	125340	119834	95.61	191	19014129	18475501	97.17
	23	74630	73850	98.95	325	18475496	18350279	99.32
simLC-36m	25	69028	68731	99.57	279	16751244	16697244	99.68
	27	68245	68010	99.66	206	14123037	14087137	99.75
	29	52885	52765	99.77	302	10562147	10545749	99.84
	31	26382	26339	99.84	2363	7276731	7272359	99.94
	33	27332	27306	99.9	340	6214325	6211238	99.95
	C	119667	112827	94.28	493	34920211	34050685	97.51
	C-21	100852	98658	97.82	566	31992027	31595445	98.76
	21	183383	178586	97.38	161	24663986	24173013	98.01
	23	106981	106133	99.21	324	24661676	24510881	99.39
simMC-36m	25	88466	88122	99.61	419	23280192	23216974	99.73
	27	78074	77825	99.68	569	21119299	21075047	99.79
	29	75800	75571	99.7	400	18839097	18777496	99.67
	31	114336	113948	99.66	168	17128489	17050171	99.54
	33	156709	156272	99.72	78	12688930	12646726	99.67
	C	73480	55508	75.54	138	10007373	7649152	76.44
	C-21	39196	35369	90.24	131	5366108	4823423	89.89
	21	51371	36693	71.43	142	6923506	5037993	72.77
	23	28614	25707	89.84	137	4132863	3703686	89.62
simHC-36m	25	17418	16557	95.06	122	2289332	2179104	95.19
	27	9822	9524	96.97	109	1184664	1149541	97.04
	29	5309	5211	98.15	102	603680	593152	98.26
	31	3047	3005	98.62	93	315736	311501	98.66
	33	1895	1885	99.47	77	162625	161704	99.43
	C	25742	25359	98.51	1223	9985001	9913743	99.29
	21	24883	24709	99.3	544	6660066	6627437	99.51
	23	20550	20459	99.56	847	6560491	6545844	99.78
EcoliStrains-10m	25	19570	19506	99.67	933	6370414	6356780	99.79
	27	17474	17422	99.7	1195	5995915	5986494	99.84
	29	17338	17278	99.65	925	5560578	5550393	99.82
	31	25468	25436	99.87	317	5237879	5233758	99.92

simLC-36m, simMC-36m, simHC-36m are the results for the low, medium and high complexity datasets with 36 million reads, respectively. EcoliStrains-10m are the results for the co-assembly strain dataset with 10 million reads. C shows the clustering results after pooling contigs obtained from running ABYSS with k ranging from 21 to 33. C-21 shows the clustering results after excluding the contigs obtained by running ABYSS for k = 21.

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ISSN: 1471-2164

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