LRScaf: improving draft genomes using long noisy reads

BMC Genomics

Table 1 Descriptive statistics of datasets for the experiment

Species	Type	Total bases (bp)	Coverage	Median (bp)	Longest (bp)	Source
E. coli	Illumina	350,000,031	70.0 X	100	100	ERA000206
	Illumina ^a	256,927,500	54.9 X	300	300	SRR826442; SRR826444; SRR826446; SRR826450
	PacBio	93,994,356	20.1 X	8712	41,331	SRX669475; SRX533603
	Nanopore ^{(2D) a}	136,895,083	29.2 X	6153	43,600	http://gigadb.org/dataset/100102
	Nanopore ^{(Full) b}	21,972,483	4.7 X	5743	47,422	ERX708228
	Nanopore ^{(All) b}	158,867,566	34.0 X	6086	47,422	ERX708228
	Nanopore ^{(Raw) b}	311,558,723	66.5 X	3557	94,116	ERX708228
S. cerevisiae	Illumina	1,268,786,706	105.1 X	202	202	SRR527545; SRR527546
	PacBio	249,319,042	20.7 X	4554	27,575	SRX533604
	Nanopore ^{(Nanocorr) b}	526,588,732	43.6 X	5512	72,879	SRP055987
	Nanopore ^{(Raw) b}	2,392,848,698	198.2 X	5059	191,145	SRP055987
A. thaliana ^(KBS-Mac-74)	Illumina	8,420,975,500	70.3 X	250	250	ERR2173372
A. thaliana ^(KBS-Mac-74)	Nanopore	3,421,779,258	28.6 X	7543	269,087	ERR2173373
A. thaliana ^(ler-0)	Illumina ^a	6,919,422,000	59.0 X	300	300	http://schatzlab.cshl.edu/data/ectools/
A. thaliana ^(ler-0)	PacBio ^a	2,400,246,920	20.5 X	15,357	41,753	http://schatzlab.cshl.edu/data/ectools/
O. sativa	Illumina	43,519,132,800	111.5 X	150	150	PRJNA515358 ^c
O. sativa	PacBio	7,999,992,602	20.5 X	4117	50,493	PRJNA318714
S. pennellii	Illumina	39,007,839,296	42.6 X	311	311	PRJEB19787
S. pennellii	Nanopore	27,483,806,911	30.0 X	13,061	15,387	PRJEB19787
Z. mays	PacBio	49,999,992,839	23.7 X	1347	17,784	PRJNA10769
H. sapiens ^(CHM1)	PacBio	59,999,995,767	20.0 X	1569	208,628	SAMN02744161
H. sapiens ^(NA12878)	Nanopore	114,380,310,980	35.0 X	4569	1,537,349	PRJEB23027

Note: ^a refers to DBG2OLC dataset; ^b refers to LINKS dataset; ^c the dataset was sequenced in this study

ISSN: 1471-2164