De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads

Table 1 Genome and transcriptome contiguity scores. Statistics for the current WTSI reference sequence are given for comparison

Description	Size (kb)	N50 (kb)	N90 (kb)	Minimum (kb)	Maximum (kb)
Description	[Contigs/genes]	[L50]	[L90]	Minimum (kb)	Maximum (kb)
WTSI reference	294,400	33.5	4.3	0.5	394.2
WTSI reference	[29,375]	[2024]	[11,638]	0.5	394.2
Uncorrected (Canu only)*	347,186	209.2	38.9	1.7	2048.3
Uncorrected (Canu only)*	[3583]	[415]	[1964]	1.7	2048.3
Trinity [de novo]	180,448	0.8	0.3	0.2	21.5
Trinity [de novo]	[291,671/172,480]**	[53,613]	[219,557]	0.2	21.5
Trinity [genome-guided]	249,065	1.2	0.3	0.2	22.0
Trinity [genome-guided]	[352,994/236,865]**	[50569]	[245,765]	0.2	22.0
Trinity [expression-filtered]	71,457	2.0	0.7	0.2	22.0
Trinity [expression-filtered]	[52,302]	[11,072]	[34,924]	0.2	22.0
WGA, Canu only	119,196	53.1	17.3	1.8	388.2
WGA, Canu only	[3280]	[647]	[2199]	1.8	388.2

WGA whole-genome amplification, WTSI Wellcome Trust Sanger Institute
*Local read correction has minimal effect on the contiguity statistics
**In the absence of expert curation, these values are patently overestimates (e.g., in the genome-guided assembly, genes near structural variant forks will be counted more than once)

ISSN: 1741-7007