RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

BMC Bioinformatics

Table 4 The influence of read coverage on the detection effect of each tools

Species	Method	Cov/read_len (bp)	Num	MA_ratio (%)	Max/min	N50 (bp)	N90 (bp)
\(Homo \ sapiens\) chr14	RepAHR	30X/100	33	100.0	833/100	286	108
	RepAHR	60X/100	32	100.0	855/100	238	126
	RepAHR	90X/100	35	100.0	1087/100	238	116
	RepAHR	120X/100	30	100.0	2057/100	238	116
	REPdenovo	30X/100	13	100.0	5079/72	5079	173
	REPdenovo	60X/100	13	100.0	5079/72	5079	147
	REPdenovo	90X/100	9	100.0	5079/76	5079	198
	REPdenovo	120X/100	11	100.0	5078/79	5078	173
	RepARK Velvet	30X/100	419	99.82	382/29	99	0
	RepARK Velvet	60X/100	545	99.76	430/29	104	0
	RepARK Velvet	90X/100	569	99.82	430/29	102	0
	RepARK Velvet	120X/100	1992	99.85	1249/29	119	64

\('Cov/read\_len\, (bp)'\) indicates the average coverage of sequencing and the average length of reads. \('Num'\) indicates the number of repeats. \('MA\_ratio\, (\%)'\) represents the multiple alignment ratio of repeats. \('Max'\) represents the length of the longest segment in the repeats. \('Min'\) represents the length of the shortest segment in detected repetitive segments. \('N50\,or\,N90'\) represents the length of the longest segment such that all the segments longer than this segment cover at least 50% or 90% of the total length of the assemblies

ISSN: 1471-2105