Light-RCV: a lightweight read coverage viewer for next generation sequencing data

BMC Bioinformatics

Table 1 Time comparison of NGS viewers.

Frequency	Savant	Tablet	IGV	Light-RCV
Per NGS experiment¹
Saccharomyces cerevisiae	0.00 ± 0.00	0.00 ± 0.00	0.00 ± 0.00	56.12 ± 1.07
Per loading an NGS experiment²
Saccharomyces cerevisiae	3.71 ± 0.22	11.79 ± 0.48	9.94 ± 0.55	0.00 ± 0.00
Per visualization of a genomic region³
1 kb genomic region	0.44 ± 0.10	(1.08 ± 0.12)	1.37 ± 0.28	0.33 ± 0.02
2 kb genomic region	0.39 ± 0.09	(1.08 ± 0.16)	1.17 ± 0.13	0.33 ± 0.03
5 kb genomic region	0.53 ± 0.09	(1.01 ± 0.17)	1.10 ± 0.12	0.37 ± 0.01
10 kb genomic region	0.77 ± 0.08	(1.07 ± 0.13)	1.16 ± 0.11	0.38 ± 0.04
20 kb genomic region	0.90 ± 0.08	(1.03 ± 0.12)	1.14 ± 0.14	0.43 ± 0.03
50 kb genomic region	*	(1.02 ± 0.15)	1.63 ± 0.16	0.76 ± 0.03
.1 Mb genomic region	*	(0.84 ± 0.10)	*	1.34 ± 0.06
.2 Mb genomic region	*	(0.96 ± 0.12)	*	2.47 ± 0.12
.5 Mb genomic region	*	(0.92 ± 0.12)	*	12.37 ± 0.23
Amortized processing time
20 kb genomic region	0.91 ± 0.08	(0.92 ± 0.12)	1.16 ± 0.14	0.53 ± 0.03

¹Time required by the compilation stage of Light-RCV. Other NGS viewers did not have this stage. ²Time required when the user chooses an NGS data in viewers. ³Time required when the user specifies a genomic region, which is critical to user experience. *The viewer does not show read coverage at these region.
Time is measured in seconds. Values in parentheses indicate that the corresponding NGS viewer did not display a base-level read coverage. Tablet shows a summarized read coverage in which the read counts of 500 genomic positions are averaged to a value.

ISSN: 1471-2105