Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

ABSTRACT:

Background

Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding.

Results

To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped

SUBMITTER: Kadota M 

PROVIDER: S-EPMC6952475 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature