EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends

BMC Bioinformatics

Table 2 Summary of simulated and real contig data

Assembly type	Species	Chromo-somes (n)	Genome size	Total contig number	Total contig length	Assembled percent (%)	Average contig number	Contig N50	Contig N90
Simulated assembly	Human	23	3,054,815,472	104	3,054,815,472	100%	4.52	47,909,438	14,532,355
	Rice	12	373,094,580	42	373,094,580	100%	3.50	11,071,427	5,000,429
	Arabidopsis	5	119,146,348	11	119,146,348	100%	2.20	9,660,775	5,994,203
Hifiasm-assembly	Human	23	3,054,815,472	82	3,007,080,905	98%	3.57	89,131,734	28,203,557
	Great burdock	18	1,720,000,000	30	1,709,056,189	99%	1.67	74,692,580	38,981,084
	Water spinach	15	485,000,000	29	480,197,403	99%	1.61	23,511,778	9,860,712

Genome size are validated or estimated value. The contigs with size > 1 Mb are used for statistics in this table. Assembled percent = total contig length/genome size. Average contig number means average contig number per chromosome. For simulated data, the reference genomes of human CHM13 v1.1, rice (Nipponbare) ASM386523v1, Arabidopsis thaliana (Columbia) TAIR10.1 were used to simulate large contigs, and each chromosome of reference genome was randomly split into 1–6 contigs. In the simulated assembly, contigs size smaller than 1 Mb were not allowed, and all the contigs are larger than 1 Mb. For real data, the hifiasm-assembled contigs of human were downloaded from https://zenodo.org/record/4393631/files/CHM13.HiFi.hifiasm-0.12.fa.gz, while the contigs of great burdock and water spinach were assembled by hifiasm using default parameters from HiFi reads downloaded from NCBI-SRA databases (PRJNA764011 and PRJNA764042)

ISSN: 1471-2105