BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Nikolenko, Sergey I; Korobeynikov, Anton I; Alekseyev, Max A

doi:10.1186/1471-2164-14-S1-S7

BMC Genomics

Table 2 Assembly results, single-cell E.coli and S. aureus datasets (contigs of length ≥ 200 are used).

From: BayesHammer: Bayesian clustering for error correction in single-cell sequencing

Statistics	BayesHammer	BayesHammer(scaff old)	Coral	Coral (scaff old)	EulerSR	EulerSR (scaff old)	Hammer, expanded	Hammer, no expansion	Hammer, no expansion(scaff old)	Hammer(scaff old)
	Single-cell E. coli, reference length 4639675, reference GC content 50.79%
# contigs (1000 bp)	191	158	276	224	231	150	195	282	242	173
# contigs	521	462	675	592	578	375	529	655	592	477
Largest contig	269177	284968	179022	179022	267676	267676	268464	210850	210850	268464
Total length	4952297	4989404	5064570	4817757	4817757	4902434	4977294	5097148	5340871	5005022
N50	110539	113056	45672	67849	74139	95704	97639	65415	84893	109826
NG50	112065	118432	55073	87317	77762	108976	101871	68595	96600	112161
NA50	110539	113056	45672	67765	74139	95704	97639	65415	84841	109826
NGA50	112064	118432	55073	87317	77762	108976	101871	68594	96361	112161
# misassemblies	4	6	9	12	6	8	4	4	7	7
# misassembled contigs	4	6	9	10	6	8	4	4	7	7
Misass. contigs length	42496	94172	62114	150232	47372	149639	43304	26872	147140	130706
Genome covered (%)	96.320	96.315	96.623	96.646	95.337	95.231	96.287	96.247	96.228	96.281
GC (%)	49.70	49.69	49.61	49.56	49.90	49.74	49.68	49.64	49.60	49.68
# mismatches/100 kbp	11.22	11.70	8.36	9.10	5.55	5.82	12.77	54.11	52.48	13.08
# indels/100 kbp	1.07	8.26	9.17	12.76	0.52	47.80	0.91	1.17	7.96	8.69
# genes	4065 +	4079 +	3998 +	4040 +	3992 +	4020 +	4068 +	4034 +	4048 +	4078 +
	124 part	110 part	180 part	143 part	140 part	107 part	123 part	152 part	136 part	111 part
	Single-cell *S. aureus*, reference length 2872769, reference GC content 32.75%
# contigs (1000 bp)	95	85	132	113	82	70	114	272	258	101
Total length (1000 bp)	3019597	3309342	3055585	3066662	2972925	2993100	3033912	3389846	3405223	3509555
# contigs	260	241	455	423	166	134	312	721	711	292
Largest contig	282558	328686	208166	208166	254085	535477	282558	148002	166053	328679
Total length	3081173	3368034	3160497	3166169	3008746	3020256	3111423	3575679	3594468	3584266
N50	87684	145466	62429	90701	101836	145466	74715	30788	34943	131272
NG50	112566	194902	87636	99341	108151	159555	88292	39768	45889	180022
NA50	87684	145466	62429	89365	100509	145466	68711	30788	34552	112801
NGA50	88246	148064	74452	90101	101836	145466	88289	35998	42642	148023
# misassemblies	15	17	11	14	4	5	11	14	18	14
# misassembled contigs	12	14	9	10	4	5	9	14	16	12
Misass. contigs length	340603	779785	478009	523596	377133	918380	402997	272677	324361	940356
Genome covered (%)	99.522	99.483	99.449	99.447	99.213	99.254	99.204	98.820	98.888	99.221
GC (%)	32.67	32.63	32.64	32.63	32.66	32.67	32.67	32.39	32.38	32.57
# mismatches per 100 kbp	3.18	8.01	12.44	12.65	9.72	10.28	17.38	54.92	55.50	15.36
# indels per 100 kbp	2.17	2.30	15.50	15.67	3.80	4.08	3.57	2.64	2.72	3.04
# genes	2540 +	2547 +	2532 +	2540 +	2547 +	2550 +	2535 +	2477 +	2485 +	2539 +
	36 part	30 part	45 part	37 part	30 part	27 part	41 part	91 part	85 part	38 part

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ISSN: 1471-2164

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