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

BMC Bioinformatics

Table 2 Metrics of alignment segments

Species	Segment type	Num	N50 (bp)	Avg length (bp)	Max (bp)	AR (%)
Drosophila melanogaster	High-frequency k-mers	4105	1291	187.36	8256	58.90
Drosophila melanogaster	High-frequency reads	1336	3336	542.81	8256	80.55
Mus musculus	High-frequency k-mers	2612	1142	262.49	7673	24.73
Mus musculus	High-frequency reads	421	5943	1203.55	7673	82.64
\(Homo \ sapiens\) chr14	High-frequency k-mers	1481	239	112.05	6064	38.32
\(Homo \ sapiens\) chr14	High-frequency reads	242	394	338.63	6064	75.23

\('Num'\) indicates the number of alignment segments. \('N50'\) indicates the length of the longest segment such that all the segments longer than this segment cover at least 50% of the total length of all segments. \('Avg\,Length (bp)'\) indicates the average length of segments. \('Max'\) indicates the maximum length of a repeat. \('AR (\%)'\) indicates alignment ratio of the high-frequency k-mers or the high-frequency reads on Repbase sequences

ISSN: 1471-2105