Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies
| Autor: | Yuta Ohishi, Shigehiro Kuraku, Kazuaki Yamaguchi, Osamu Nishimura, Yuki Naito, Mitsutaka Kadota |
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| Rok vydání: | 2021 |
| Předmět: |
Paroedura picta
Scaffold Genome Computer science Genome sequence assembly Scale (chemistry) Computational biology Genomics Biology Pipeline (software) Chromatin Chromosomes Chromosome conformation capture Chromosome (genetic algorithm) Genetics Madagascar Animals Ecology Evolution Behavior and Systematics Genome scaffolding |
| Zdroj: | Molecular ecology. 30(23) |
| ISSN: | 1365-294X |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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