Technical considerations in Hi-C scaffolding and evaluation of
chromosome-scale genome assemblies
The recent development of ecological studies has been fueled by the
introduction of massive information based on chromosome-scale genome
sequences, even for species for which genetic linkage is not accessible.
This was enabled mainly by the application of Hi-C, a method for
genome-wide chromosome conformation capture that was originally
developed for investigating the long-range interaction of chromatins.
Performing genomic scaffolding using Hi-C data is highly
resource-demanding and employs elaborate laboratory steps for sample
preparation. It starts with building a primary genome sequence assembly
as an input, which is followed by computation for genome scaffolding
using Hi-C data, requiring careful validation. This article presents
technical considerations for obtaining optimal Hi-C scaffolding results
and provides a test case of its application to a reptile species, the
Madagascar ground gecko (Paroedura picta). Among the metrics that are
frequently used for evaluating scaffolding results, we investigate the
validity of the completeness assessment of chromosome-scale genome
assemblies using single-copy reference orthologs, and report problems of
the widely used program pipeline BUSCO.