Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
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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 improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage.
Conclusions
This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.
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Now published in GigaScience doi: 10.1093/gigascience/giz158
Mitsutaka Kadota 1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mitsutaka KadotaHisashi Miura 2Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Hisashi MiuraKaori Tanaka 1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan3Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on …
Now published in GigaScience doi: 10.1093/gigascience/giz158
Mitsutaka Kadota 1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mitsutaka KadotaHisashi Miura 2Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Hisashi MiuraKaori Tanaka 1Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan3Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteIchiro Hiratani 2Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe, 650-0047, JapanFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Ichiro Hiratani
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz158 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102051 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102052 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102053
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