PacBio의 HiFi read는 99% 이상의 high accuracy의 long read 데이터를 제공함으로써, Genome assembly에 필수적인 시퀀싱 기술입니다. High accuracy의 long HiFi read는 다양한 application에 사용되어 질 수 있으며, 특히 genome assembly에 있어 최적의
결과를 얻으실 수 있습니다.
이번 세미나에서는 PacBio HiFi read를 적용한 실제연구사례를 소개드리고자 합니다.
본 웨비나는 아래와 같은 내용으로 한국어로 진행됩니다.
1. PacBio의 HiFi read를 이용한 Genome assembly에 대한 간략한 소개
2. HiCanu 기반으로 Telomere-to-Telomere assembly 구축 및 개선하는 방법
HiCanu: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Sergey Nurk, Brian P. Walenz, Arang Rhie, Mitchell R. Vollger, Glennis A, Logsdon, Robert Grothe, Karen H. Miga, Evan E. Eichler, Adam M. Phillippy, Sergey Koren. Genome Research. Published in Advance August 14, 2020, doi: 10.1101/gr.263566.120 Genome Res. 2020. © 2020 Nurk et al.; Published by Cold Spring Harbor Laboratory Press
Telomere-to-telomere assembly of a complete human X chromosome. Karen H. Miga, Sergey Koren, Arang Rhie, Mitchell R. Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A. Logsdon, Valerie A. Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G. Bouffard, Alexander M. Chang, Nancy F. Hansen, Amy B. Wilfert, Françoise Thibaud-Nissen, Anthony D. Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y. Dennis, Daniela C. Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J. Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, Rosa ana Risques, Tina A. Graves Lindsay, Robert Fulton, Ira Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, James C. Mullikin, Pavel A. Pevzner, Jennifer L. Gerton, Beth A. Sullivan, Evan E. Eichler & Adam M. Phillippy. Nature. Published 14 July 2020. 585, pages79–84(2020)
Date & Time : 2020년 9월 23일 수요일, 오전 10시 (한국시간)
이아랑 (Arang Rhie), Ph.D.
Genome Informatics Section
CSGB, NHGRI, NIH
Title : 완벽을 추구하며 : 텔로미어-텔로미어 어셈블리 검증 및 개선
Abstract : Over the past summer, the telomere-to-telomere (T2T) consortium held a workshop to finish the entire genome of CHM13, a nearly haploid human cell line. The newly constructed assembly resolves centromeres, human satellites, and segmental duplications. These regions had remained unresolved despite the multi-decade effort to finish the human genome. Given this assembly, we now face a new challenge: how can we validate these regions? If there are errors, how do we find them and correct them? While finalizing the CHM13 T2T assembly, I was leading the polishing team which explored both read alignments and alignment-free strategies to identify and distinguish errors from true heterozygous variants. Accurate identification of errors required the application of novel repeat-aware and marker-assisted methods for correctly mapping long reads to the assembly. This allowed single nucleotide and structural variant calling within the most complex regions of the genome. However, due to the high quality of the initial assembly, and the small number of corrections needed, we required a highly specific “do no harm” polishing approach. Thus, we developed a new k-mer-assisted method for guiding the correction of small errors identified by either short or long-read variant calls. This approach successfully identified a few thousands of true heterozygous variants in addition to targets for correction. Hi-C and Strand-Seq data further confirmed the structural integrity of the assembly. Integration of all available technologies ultimately allowed the construction of a near-perfect consensus sequence with an estimated error rate of less than one per million bases.박지영 (Jiyoung Park)
Title: Long HiFi reads for high-quality genome assemblies
Abstract: PacBio is the only sequencing technology to offer highly accurate long reads (HiFi reads) that provide Sanger-quality accuracy (>99%) with the read lengths needed for assembly of complex genomes. The long length and high accuracy of HiFi reads makes them the ideal starting point for many applications, and one area of major interest is genome assembly.