Disk-based k-mer counting on a PC

BMC Bioinformatics

Table 1 Statistics of the datasets used in the experiments for k=25

	D. ananassae	C. elegans	Z. mays	H. sapiens	H. sapiens
				NA19238	HG02057
FASTQ file size [GB]	8.7	16.4	45.9	353	208
Total gzipped size [GB]	1.8	4.6	16.3	116.6	65.9
No. of gzipped files	6	2	108	463	6
No. of reads [ ×10⁶]	35	68	62	2,662	860
Read lengths	75	100	25-2043	36(most)-75	100
		Statistics of k -mers
No. of singletons	43	347	1,010	11,823	3,367
No. of distinct	63	459	1,916	14,599	6,023
No. of distinct non-singletons	20	112	906	2,776	2,657
Total no.	1,803	5,127	20,214	44,687	65,325

ISSN: 1471-2105