  Motivation: The application of PacBio HiFi and ultra-long ONT reads have
achieved huge progress in the contig-level assembly, but it is still
challenging to assemble large contigs into chromosomes with available Hi-C
scaffolding software, which all compute the contact value between contigs using
the Hi-C links from the whole 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 present a software package EndHiC, which is suitable to assemble
large contigs (> 1-Mb) into chromosomal-level scaffolds, using Hi-C links from
only the contig end regions instead of the whole contig regions. Benefiting
from the increased signal to noise ratio, EndHiC achieves much higher
scaffolding accuracy compared to existing software LACHESIS, ALLHiC, and
3D-DNA. Moreover, EndHiC has few parameters, runs 10-1000 times faster than
existing software, needs trivial memory, provides robustness evaluation, and
allows graphic viewing of the scaffold results. The high scaffolding accuracy
and user-friendly interface of EndHiC, liberate the users from labor-intensive
manual checks and revision works.
  Availability and implementation: EndHiC is written in Perl, and is freely
available at https://github.com/fanagislab/EndHiC. Contact<EMAIL_ADDRESS>and
<EMAIL_ADDRESS>Supplementary information: Supplementary data are available
at Bioinformatics online.
