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PGP1 personal genome assembly - a hybrid assembly dataset using ONT’s PromethION and PacBio’s HiFi sequencing

View ORCID ProfileHui-Su Kim, Changjae Kim, View ORCID ProfileGeorge Church, View ORCID ProfileJong Bhak
doi: https://doi.org/10.1101/2021.09.03.458806
Hui-Su Kim
1Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Ulju-gun, Eonyang-eup, 44919, Republic of Korea
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Changjae Kim
2Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Ulju-gun, Eonyang-eup, 44919, Republic of Korea
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George Church
3Department of Genetics, New Research Building (NRB), 77 Avenue Louis Pasteur, Boston, MA 02115 USA
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Jong Bhak
1Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Ulju-gun, Eonyang-eup, 44919, Republic of Korea
2Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Ulju-gun, Eonyang-eup, 44919, Republic of Korea
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  • For correspondence: jongbhak@genomics.org
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Abstract

PGP1 is the first participant of Personal Genome Project. We present the PGP1’s chromosome-scale genome assembly. It was constructed using 255 Gb ultra-long PromethION reads and 97 Gb short paired-end reads. For reducing base calling errors, we corrected PromethION reads using 72 Gb PacBio HiFi reads. 327 Gb Hi-C chromosomal mapping data were utilized to maximize the assembly’s contiguity. PGP1’s contig assembly was 3.01 Gb in length comprising of 4,234 contigs with an N50 value of 33.8 Mb. After scaffolding with Hi-C data and extensive manual curation, we obtained a chromosome-scale assembly that represents 3,880 scaffolds with an N50 value of 142 Mb. From the Merqury assessment, PGP1 assembly achieved a high QV score of Q45.45. For a gene annotation, we predicted 106,789 genes with a liftover from the Gencode 38 and an assembly of transcriptome data.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://genomics.org/PGP1

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 05, 2021.
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PGP1 personal genome assembly - a hybrid assembly dataset using ONT’s PromethION and PacBio’s HiFi sequencing
Hui-Su Kim, Changjae Kim, George Church, Jong Bhak
bioRxiv 2021.09.03.458806; doi: https://doi.org/10.1101/2021.09.03.458806
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PGP1 personal genome assembly - a hybrid assembly dataset using ONT’s PromethION and PacBio’s HiFi sequencing
Hui-Su Kim, Changjae Kim, George Church, Jong Bhak
bioRxiv 2021.09.03.458806; doi: https://doi.org/10.1101/2021.09.03.458806

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