An improved filtering algorithm for big read datasets and its application to single-cell assembly

Wedemeyer, Axel; Kliemann, Lasse; Srivastav, Anand; Schielke, Christian; Reusch, Thorsten B.; Rosenstiel, Philip

doi:10.1186/s12859-017-1724-7

BMC Bioinformatics

Table 5 Filter and assembly statistics for Bignorm with Q ₀=20, Diginorm, and the raw datasets (Part II)

From: An improved filtering algorithm for big read datasets and its application to single-cell assembly

Dataset	Algorithm	N50			Longest contig length			Genomic fraction			Misassembled contig length
		abs	% of raw	% of Diginorm	abs	% of raw	% of Diginorm	abs	% of raw	% of Diginorm	abs	% of raw	% of Diginorm
Aceto	Bignorm	2324	79	105	11,525	98	100	91	97	97	52,487	148	178
	Diginorm	2216	76		11,525	98		94	100		29,539	84
	Raw	2935			11,772			94			35,351
Alphaproteo	Bignorm	11,750	94	115	43,977	91	95	98	101	105	52,001	120	89
	Diginorm	10,213	82		46,295	95		93	95		58,184	134
	Raw	12,446			48,586			98			43,388
Arco	Bignorm	3320	81	97	12,808	57	57	85	100	97	76,797	99	91
	Diginorm	3434	84		22,463	100		88	103		84,613	109
	Raw	4092			22,439			85			77,888
Arma	Bignorm	18,432	102	107	108,140	100	100	98	100	100	774,291	91	103
	Diginorm	17,288	96		108,498	100		98	100		748,560	88
	Raw	18,039			108,498			98			849,085
ASZN2	Bignorm	19,788	91	88	72,685	71	88	97	99	99	2,753,167	94	105
	Diginorm	16,591	76		82687	81		97	100		2,617,095	89
	Raw	21,784			102,287			97			2,941,524
Bacteroides	Bignorm	3356	68	100	25,300	100	100	95	98	99	70,206	105	112
	Diginorm	3356	68		25,300	100		96	99		62,882	94
	Raw	4930			25,299			98			66,626
Caldi	Bignorm	50,973	82	83	143,346	89	91	100	100	100	573,836	94	68
	Diginorm	61,108	98		157,479	98		100	100		839,126	138
	Raw	62,429			160,851			100			609,604
Caulo	Bignorm	4515	69	95	20,255	100	107	96	98	98	60,362	86	113
	Diginorm	4729	72		18,907	93		98	101		53,456	76
	Raw	6562			20,255			97			70,161
Chloroflexi	Bignorm	13,418	102	109	79,605	102	102	99	100	100	666,519	95	93
	Diginorm	12,305	93		78,276	100		100	100		716,473	102
	Raw	13,218			78,276			99			703,171
Crenarch	Bignorm	6538	77	91	31,401	81	66	97	99	99	484,354	89	95
	Diginorm	7148	84		47,803	124		98	100		510,256	94
	Raw	8501			38,582			98			544,763
Cyanobact	Bignorm	5833	95	99	33,462	98	100	99	101	100	236,391	113	110
	Diginorm	5907	96		33,516	98		99	101		214,574	103
	Raw	6130			34,300			98			209,269
E. coli	Bignorm	112,393	100	100	268,306	94	94	96	100	100	28,966	65	65
	Diginorm	112,393	100		285,311	100		96	100		44,465	100
	Raw	112,393			285,528			96			44,366
SAR324	Bignorm	135,669	100	114	302,443	100	100	99	100	100	4,259,479	98	100
	Diginorm	119,529	88		302,443	100		99	100		4,264,234	98
	Raw	136,176			302,442			99			4,342,602

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com