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

Abstract

Background The application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still challenging to assemble large contigs into chromosomes with available Hi-C scaffolding tools, which count Hi-C links between contigs using the whole or a large part of contig regions. As the Hi-C links of two adjacent contigs concentrate only at the neighbor ends of the contigs, larger contig size will reduce the power to differentiate adjacent (signal) and non-adjacent (noise) contig linkages, leading to a higher rate of mis-assembly. Results We design and develop a novel Hi-C based scaffolding tool EndHiC, which is suitable to assemble large contigs into chromosomal-level scaffolds. The core idea behind EndHiC, which distinguishes it from other Hi-C scaffolding tools, is using Hi-C links only from the most effective regions of contig ends. By this way, the signal neighbor contig linkages and noise non-neighbor contig linkages are separated more clearly. Benefiting from the increased signal to noise ratio, the reciprocal best requirement, as well as the robustness evaluation, EndHiC achieves higher accuracy for scaffolding large contigs compared to existing tools. EndHiC has been successfully applied in the Hi-C scaffolding of simulated data from human, rice and Arabidopsis, and real data from human, great burdock, water spinach, chicory, endive, yacon, and Ipomoea cairica, suggesting that EndHiC can be applied to a broad range of plant and animal genomes. Conclusions EndHiC is a novel Hi-C scaffolding tool, which is suitable for scaffolding of contig assemblies with contig N50 size near or over 10 Mb and N90 size near or over 1 Mb. EndHiC is efficient both in time and memory, and it is interface-friendly to the users. As more genome projects have been launched and the contig continuity constantly improved, we believe EndHiC has the potential to make a great contribution to the genomics field and liberate the scientists from labor-intensive manual curation works.

Chromosome-level genome of a leaf vegetableGlebionis coronariaprovides insights into the biosynthesis of monoterpenoids contributing to its special aroma

“…The assembly size is similar to the estimated genome size, suggesting high completeness of the genome assembly. Then, 85.2% of these contigs were further anchored into nine pseudochromosomes by EndHiC, 24 with scaffold N50 size of 610.7 Mb ( Table 1 , Supplementary Tables S2 and S3 , Supplementary Fig. S3 ).…”

“…To obtain the nine pseudochromosome scaffolds of G. coronaria through proximity ligation data, we mapped the quality-filtered Hi-C sequencing reads to the reference genome to generate the valid Hi-C contact matrixes among contig bins (size 100,000 bp) using HiC-Pro version 3.1.0. 23 Then, the contigs >1,000,000 bp were assembled into chromosome-level scaffolds based on the Hi-C linkage information among contig ends, using EndHiC version 1.0 24 in multi-round mode and manual correction of mis-joined scaffolds according to Hi-C heatmap.…”

Haplotype‐resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

“…De novo assembly of two haplotype genomes based on PacBio long reads and Hi‐C data was performed using hifiasm v0.16.1‐r375 (Cheng et al., 2021) with the default parameters. These two haplotypes were first assembled at the chromosome level using ALLHiC v0.9.13 (Zhang, et al., 2019) and EndHiC v1.0 (Wang et al., 2022), but both were found to be poorly assembled. So that we aligned the two haplotypes derived from hifiasm using Minimap2 v2.17‐r941 (Li, 2018), then extracted the corresponding contigs and sorted into the chromosome‐level haplotype genomes.…”

A chromosome-level reference genome of a Fabaceae species yam bean (Pachyrhizus erosus)

“…The pseudo-chromosomes were constructed using Hi-C sequencing data. We used HiC-Pro v2.11.4 (Servant et al ., 2015) pipeline to perform the Hi-C reads mapping, valid ligation pairs detection, and the Hi-C link matrixes generation, which were further used for pseudo-chromosomes construction by EndHiC v1.0 (Wang et al ., 2022). The completeness of the genome assembly was estimated using BUSCO v5.2.2 (BUSCO) (Simao et al ., 2015) against embryophyta_odb10 database.…”