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

Mitsutaka Kadota | Zendy; Osamu Nishimura | Zendy; Hisashi Miura | Zendy; Kaori Tanaka | Zendy; Ichiro Hiratani | Zendy; Shigehiro Kuraku | Zendy

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

Author(s) -

Mitsutaka Kadota,

Osamu Nishimura,

Hisashi Miura,

Kaori Tanaka,

Ichiro Hiratani,

Shigehiro Kuraku

Publication year - 2020

Publication title -

gigascience

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.947

H-Index - 54

ISSN - 2047-217X

DOI - 10.1093/gigascience/giz158

Subject(s) - scaffold , genome , computational biology , chromosome , benchmarking , sample (material) , protocol (science) , computer science , biology , genetics , gene , chemistry , medicine , marketing , database , pathology , business , alternative medicine , chromatography

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.

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