Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

Wetzel, Joshua; Kingsford, Carl; Pop, Mihai

doi:10.1186/1471-2105-12-95

BMC Bioinformatics

Table 4 Results of SOAPdenovo assemblies

From: Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

Organism	Libs	Num	Total Size	Min Size	Max Size	Avg Size	Median Size	N50
Acinetobacter baumanii	200	6327	4064963	68	37142	642.48	100	7905
	200+6000	8192	4003114	33	29829	488.66	100	2455
	165	6991	4032232	40	18098	576.77	100	3653
	165+276	6014	4069844	26	48396	676.73	100	12063
	454	8544	4015574	33	20322	469.99	100	2919
	454+1708	8038	4069168	33	21003	506.24	100	3425
Bacillus anthracis	200	9102	5928608	33	48738	651.35	100	7943
	200+6000	10302	5884980	23	28576	571.25	100	4948
	157	10654	5865861	21	15749	550.58	100	2872
	157+451	9184	5956270	12	43427	648.55	100	9257
	464	12716	5831216	33	14895	458.57	100	2724
	464+839	16578	5686718	32	12862	343.03	100	1204
Bacteroides thetaiotaomicron	200	11092	7094608	34	49008	639.61	100	8114
	200+6000	12638	7044065	33	31728	557.37	100	4418
	159	12993	7033473	94	19688	541.33	100	2941
	159+297	11024	7133929	38	63771	647.13	100	10826
	462	15383	6975016	32	15352	453.42	100	2747
	462+1759	13948	7106347	32	22002	509.49	100	3703
Deinococcus radiodurans	200	5222	3053941	11	57264	584.82	100	7449
	200+6000	6436	2975712	33	10788	462.35	100	2142
	145	6166	2977456	21	12433	482.88	100	1952
	145+745	7033	2957901	16	13154	420.57	100	1715
	485	7822	2962094	22	11751	378.69	100	1744
	485+930	9452	2892284	26	11512	306	100	913
Mycobacterium tuberculosis	200	8906	5075368	31	25729	569.88	100	6301
	200+6000	11220	4978074	23	17275	443.68	100	2095
	155	10022	4996604	25	18585	498.56	100	2520
	155+288	12160	4931391	33	12018	405.54	100	1544
	491	12851	4959477	32	11915	385.92	100	1929
	491+824	12285	5065937	33	19438	412.37	100	2368
Rickettsia prowazekii	200	1933	1275800	58	34779	660.01	100	8633
	200+6000	2455	1254405	33	21498	510.96	100	2782
	170	2064	1258665	100	16628	609.82	100	4242
	170+288	1846	1275767	38	47307	691.1	100	11463
	467	2639	1255736	33	16084	475.84	100	2833
Staphylococcus aureus	200	5099	3240933	20	34464	635.6	100	7206
	200+6000	6428	3177307	33	18574	494.29	100	2465
	154	6066	3202427	16	17004	527.93	100	2602
	154+436	5089	3263973	20	62134	641.38	100	9162
	461	6940	3184253	33	20378	458.83	100	2783
	461+943	6466	3242406	33	19545	501.45	100	3498
Vibrio parahaemolyticus	200	3396	2151560	100	48275	633.56	100	8169
	200+6000	4238	2119692	34	16163	500.16	100	2697
	161	3897	2129657	65	16127	546.49	100	3125
	161+298	3350	2159809	35	45188	644.72	100	10626
	440	4304	2128652	32	17300	494.58	100	3567

Contig statistics for various assemblies using SOAPdenovo with 'tuned' and 'standard' mate-pair libraries. The standard sizes used were always 200 bp inserts or a combination of 200 bp and 6000 bp inserts. Tuned sizes varied according to the prediction of ideal mate-pair sizes provided by analysis of our 35-mer and 100-mer graphs (corresponding to sizes listed in Table 3). All assemblies used 30× coverage with 100 bp reads created by MetaSim. The best assembly (in terms of N50 contig size) for each organism is bold-faced.

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ISSN: 1471-2105

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