Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

BMC Bioinformatics

Table 1 Summary of search space per k-mer size and number of k-mers found in datasets

k-mer size	# Canonical k-mer combinations	% of k-mers found per sample		% of k-mers found per sample, shared by at least two samples
k-mer size	# Canonical k-mer combinations	Median	MAD	Median	MAD
11-mer	2.10 × 10⁰⁶	100.00 %	1.58 %	100.00 %	0.00 %
15-mer	5.40 × 10⁰⁸	53.59 %	17.07 %	100.00 %	0.00 %
17-mer	8.60 × 10⁰⁹	8.90 %	4.03 %	98.37 %	0.99 %
21-mer	2.20 × 10¹²	0.05 %	0.03 %	81.45 %	20.55 %
31-mer	2.30 × 10¹⁸	0.000000061 %	0.000000032 %	67.05 %	24.14 %

The second column contains the total number of possible k-mers, calculated as (4^{k-mer size}/2), where the division by two is due to canonization. The third column is the median and the Median Absolute Deviation (MAD) of the total number of k-mers found in the samples (Additional file 3: Table S3) divided by the number of possible k-mers, showing the percentage of combinations actually found and, consequently, the saturation of the search space; the fourth column gives the median and MAD of the percentage of valid k-mers (k-mers shared between at least two samples, Additional file 3: Table S3)

ISSN: 1471-2105