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

BMC Bioinformatics

Table 1 Metrics of repeats on five datasets

Species	Method	Num	Size (kbp)	Max/min	N50 (bp)	N90 (bp)
Drosophila melanogaster	RepARK CLC	818	518	6833/200	1040	255
	RepARK Velvet	4561	873	7587/57	285	87
	REPdenovo	52	61	8339/102	2843	397
	RepAHR	2647	1350	12,787/56	1350	98
Saccharomyces cerevisiae	RepARK CLC	545	291	8271/200	626	266
	RepARK Velvet	1457	394	9129/57	423	111
	REPdenovo	3	0.72	265/213	258	213
	RepAHR	392	219	9523/128	2089	183
Acromyrmex echinatior	RepARK CLC	485	249	8272/200	659	240
	RepARK Velvet	3931	559	5547/57	160	68
	REPdenovo	249	99	2143/100	597	182
	RepAHR	2699	514	10,701/88	285	86
\(Homo \ sapiens\) chr14	RepARK CLC	105	29	594/201	273	216
	RepARK Velvet	846	106	574/57	140	80
	REPdenovo	14	9	5545/101	5545	211
	RepAHR	1738	219	2177/45	213	61
\(Mus\ musculus\)	RepARK CLC	3839	1835	17,062/200	565	236
	RepARK Velvet	47,232	2302	16,526/57	129	57
	REPdenovo	9376	12,652	14,827/100	3129	848
	RepAHR	77,891	19,201	28,893/150	503	222

\('Num'\) indicates the number of repeats. \('Size'\) indicates the total length of all repeats. \('Max'\) represents the length of the longest segment in the repeats. \('Min'\) represents the length of the shortest segment in the repeats. \('N50\, or\, N90'\) 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