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Motivation: The application of PacBio HiFi and ultra-long ONT reads haveachieved huge progress in the contig-level assembly, but it is stillchallenging to assemble large contigs into chromosomes with available Hi-Cscaffolding software, which all compute the contact value between contigs usingthe Hi-C links from the whole contig regions. As the Hi-C links of two adjacentcontigs concentrate only at the neighbor ends of the contigs, larger contigsize will reduce the power to differentiate adjacent (signal) and non-adjacent(noise) contig linkages, leading to a higher rate of mis-assembly.  Results: We present a software package EndHiC, which is suitable to assemblelarge contigs (> 1-Mb) into chromosomal-level scaffolds, using Hi-C links fromonly the contig end regions instead of the whole contig regions. Benefitingfrom the increased signal to noise ratio, EndHiC achieves much higherscaffolding accuracy compared to existing software LACHESIS, ALLHiC, and3D-DNA. Moreover, EndHiC has few parameters, runs 10-1000 times faster thanexisting software, needs trivial memory, provides robustness evaluation, andallows graphic viewing of the scaffold results. The high scaffolding accuracyand user-friendly interface of EndHiC, liberate the users from labor-intensivemanual checks and revision works.  Availability and implementation: EndHiC is written in Perl, and is freelyavailable at https://github.com/fanagislab/EndHiC. Contact: fanwei@caas.cn andmilrazhang@163.com Supplementary information: Supplementary data are availableat Bioinformatics online.

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