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

BMC Genomics

Table 1 k-mer statistics.

Correction tool	Running time	k-mers					Reads
		Total	Genomic	Non-genomic	% of all genomic k -mers found in reads	% genomic among all k -mers in reads	% reads aligned to genome
		Multi-cell E. coli, total 4,543,849 genomic k-mers
Uncorrected		187,580,875	4,543,684	183,037,191	99.99	2.4	99.05
Quake		4,565,237	4,543,461	21,776	99.99	99.5	99.97
HammerNoExpansion	30 m	58,305,738	4,543,674	53,762,064	99.99	8.4	95.59
HammerExpanded	36 m	28,290,788	4,543,673	23,747,115	99.99	19.1	99.49
BayesHammer	37 m	27,100,305	4,543,674	22,556,631	99.99	20.1	99.62
		Single-cell *E. coli*, total 4,543,849 genomic k-mers
Uncorrected		165,355,467	4,450,489	160,904,978	97.9	2.7	79.05
Camel	2 h 29 m	147,297,070	4,450,311	142,846,759	97.9	3.0	81.25
Euler-SR	2 h 15 m	138,677,818	4,450,431	134,227,387	97.9	3.2	81.95
Coral	2 h 47 m	156,907,496	4,449,560	152,457,936	97.9	2.8	80.28
HammerNoExpansion	37 m	53,001,778	4,443,538	48,558,240	97.8	8.3	81.36
HammerExpanded	43 m	36,471,268	4,443,545	32,027,723	97.8	12.1	86.91
BayesHammer	57 m	35,862,329	4,443,736	31,418,593	97.8	12.4	87.12
		Single-cell *S. aureus*, total 2,821,095 genomic k-mers
Uncorrected		88,331,311	2,820,394	85,510,917	99.98	3.2	75.07
Camel	5 h 13 m	69,365,311	2,820,350	66,544,961	99.97	4.1	75.27
Euler-SR	2 h 33 m	58,886,372	2,820,349	56,066,023	99.97	4.8	75.24
Coral	7 h 12 m	83,249,146	2,820,011	80,429,135	99.96	3.4	75.22
HammerNoExpansion	58 m	37,465,296	2,820,341	34,644,955	99.97	7.5	71.63
HammerExpanded	1 h 03 m	23,197,521	2,820,316	20,377,205	99.97	12.1	76.54
BayesHammer	1 h 09 m	22,457,509	2,820,311	19,637,198	99.97	12.6	76.60

ISSN: 1471-2164