Polishing high-quality genome assemblies

被引:4
作者
Fang, Li [1 ]
Wang, Kai [1 ,2 ]
机构
[1] Childrens Hosp Philadelphia, Raymond G Perelman Ctr Cellular & Mol Therapeut, Philadelphia, PA 19104 USA
[2] Univ Penn, Perelman Sch Med, Dept Pathol & Lab Med, Philadelphia, PA 19104 USA
关键词
D O I
10.1038/s41592-022-01515-1
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
A repeat-aware pipeline corrects structural assembly errors and polishes assembly sequences in large repeats without overcorrection.
引用
收藏
页码:649 / 650
页数:2
相关论文
共 9 条
[1]   Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies [J].
Cartney, Ann M. Mc ;
Shafin, Kishwar ;
Alonge, Michael ;
Bzikadze, Andrey, V ;
Formenti, Giulio ;
Fungtammasan, Arkarachai ;
Howe, Kerstin ;
Jain, Chirag ;
Koren, Sergey ;
Logsdon, Glennis A. ;
Miga, Karen H. ;
Mikheenko, Alla ;
Paten, Benedict ;
Shumate, Alaina ;
Soto, Daniela C. ;
Sovic, Ivan ;
Wood, Jonathan Md ;
Zook, Justin M. ;
Phillippy, Adam M. ;
Rhie, Arang .
NATURE METHODS, 2022, 19 (06) :687-+
[2]  
Formenti G., NAT METHODS, DOI [10.1038/s41592-022-01445-y(2022, DOI 10.1038/S41592-022-01445-Y(2022]
[3]  
Jain C., NAT METHODS, DOI [10.1038/s41592-022-01457-8(2022), DOI 10.1038/S41592-022-01457-8(2022)]
[4]   The complete sequence of a human genome [J].
Nurk, Sergey ;
Koren, Sergey ;
Rhie, Arang ;
Rautiainen, Mikko ;
Bzikadze, Andrey, V ;
Mikheenko, Alla ;
Vollger, Mitchell R. ;
Altemose, Nicolas ;
Uralsky, Lev ;
Gershman, Ariel ;
Aganezov, Sergey ;
Hoyt, Savannah J. ;
Diekhans, Mark ;
Logsdon, Glennis A. ;
Alonge, Michael ;
Antonarakis, Stylianos E. ;
Borchers, Matthew ;
Bouffard, Gerard G. ;
Brooks, Shelise Y. ;
Caldas, Gina, V ;
Chen, Nae-Chyun ;
Cheng, Haoyu ;
Chin, Chen-Shan ;
Chow, William ;
de Lima, Leonardo G. ;
Dishuck, Philip C. ;
Durbin, Richard ;
Dvorkina, Tatiana ;
Fiddes, Ian T. ;
Formenti, Giulio ;
Fulton, Robert S. ;
Fungtammasan, Arkarachai ;
Garrison, Erik ;
Grady, Patrick G. S. ;
Graves-Lindsay, Tina A. ;
Hall, Ira M. ;
Hansen, Nancy F. ;
Hartley, Gabrielle A. ;
Haukness, Marina ;
Howe, Kerstin ;
Hunkapiller, Michael W. ;
Jain, Chirag ;
Jain, Miten ;
Jarvis, Erich D. ;
Kerpedjiev, Peter ;
Kirsche, Melanie ;
Kolmogorov, Mikhail ;
Korlach, Jonas ;
Kremitzki, Milinn ;
Li, Heng .
SCIENCE, 2022, 376 (6588) :44-+
[5]   A universal SNP and small-indel variant caller using deep neural networks [J].
Poplin, Ryan ;
Chang, Pi-Chuan ;
Alexander, David ;
Schwartz, Scott ;
Colthurst, Thomas ;
Ku, Alexander ;
Newburger, Dan ;
Dijamco, Jojo ;
Nguyen, Nam ;
Afshar, Pegah T. ;
Gross, Sam S. ;
Dorfman, Lizzie ;
McLean, Cory Y. ;
DePristo, Mark A. .
NATURE BIOTECHNOLOGY, 2018, 36 (10) :983-+
[6]   Accurate detection of complex structural variations using single-molecule sequencing [J].
Sedlazeck, Fritz J. ;
Rescheneder, Philipp ;
Smolka, Moritz ;
Fang, Han ;
Nattestad, Maria ;
von Haeseler, Arndt ;
Schatz, Michael C. .
NATURE METHODS, 2018, 15 (06) :461-+
[7]   Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads [J].
Shafin, Kishwar ;
Pesout, Trevor ;
Chang, Pi-Chuan ;
Nattestad, Maria ;
Kolesnikov, Alexey ;
Goel, Sidharth ;
Baid, Gunjan ;
Kolmogorov, Mikhail ;
Eizenga, Jordan M. ;
Miga, Karen H. ;
Carnevali, Paolo ;
Jain, Miten ;
Carroll, Andrew ;
Paten, Benedict .
NATURE METHODS, 2021, 18 (11) :1322-+
[8]   Fast and accurate de novo genome assembly from long uncorrected reads [J].
Vaser, Robert ;
Sovic, Ivan ;
Nagarajan, Niranjan ;
Sikic, Mile .
GENOME RESEARCH, 2017, 27 (05) :737-746
[9]   Parliament2: Accurate structural variant calling at scale [J].
Zarate, Samantha ;
Carroll, Andrew ;
Mahmoud, Medhat ;
Krasheninina, Olga ;
Jun, Goo ;
Salerno, William J. ;
Schatz, Michael C. ;
Boerwinkle, Eric ;
Gibbs, Richard A. ;
Sedlazeck, Fritz J. .
GIGASCIENCE, 2020, 9 (12)