Goodbye reference, hello genome graphs

被引:24
作者
Ameur, Adam [1 ,2 ]
机构
[1] Uppsala Univ, Sci Life Lab, Dept Immunol Genet & Pathol, Uppsala, Sweden
[2] Monash Univ, Dept Epidemiol & Prevent Med, Melbourne, Vic, Australia
关键词
10;
D O I
10.1038/s41587-019-0199-7
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Algorithms for building a variant-aware human graph genome enable fast and accurate genotyping without huge memory requirements.
引用
收藏
页码:866 / 868
页数:4
相关论文
共 10 条
[1]   Multi-platform discovery of haplotype-resolved structural variation in human genomes [J].
Chaisson, Mark J. P. ;
Sanders, Ashley D. ;
Zhao, Xuefang ;
Malhotra, Ankit ;
Porubsky, David ;
Rausch, Tobias ;
Gardner, Eugene J. ;
Rodriguez, Oscar L. ;
Guo, Li ;
Collins, Ryan L. ;
Fan, Xian ;
Wen, Jia ;
Handsaker, Robert E. ;
Fairley, Susan ;
Kronenberg, Zev N. ;
Kong, Xiangmeng ;
Hormozdiari, Fereydoun ;
Lee, Dillon ;
Wenger, Aaron M. ;
Hastie, Alex R. ;
Antaki, Danny ;
Anantharaman, Thomas ;
Audano, Peter A. ;
Brand, Harrison ;
Cantsilieris, Stuart ;
Cao, Han ;
Cerveira, Eliza ;
Chen, Chong ;
Chen, Xintong ;
Chin, Chen-Shan ;
Chong, Zechen ;
Chuang, Nelson T. ;
Lambert, Christine C. ;
Church, Deanna M. ;
Clarke, Laura ;
Farrell, Andrew ;
Flores, Joey ;
Galeev, Timur ;
Gorkin, David U. ;
Gujral, Madhusudan ;
Guryev, Victor ;
Heaton, William Haynes ;
Korlach, Jonas ;
Kumar, Sushant ;
Kwon, Jee Young ;
Lam, Ernest T. ;
Lee, Jong Eun ;
Lee, Joyce ;
Lee, Wan-Ping ;
Lee, Sau Peng .
NATURE COMMUNICATIONS, 2019, 10 (1)
[2]   Variation graph toolkit improves read mapping by representing genetic variation in the reference [J].
Garrison, Erik ;
Siren, Jouni ;
Novak, Adam M. ;
Hickey, Glenn ;
Eizenga, Jordan M. ;
Dawson, Eric T. ;
Jones, William ;
Garg, Shilpa ;
Markello, Charles ;
Lin, Michael F. ;
Paten, Benedict ;
Durbin, Richard .
NATURE BIOTECHNOLOGY, 2018, 36 (09) :875-+
[3]   Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype [J].
Kim, Daehwan ;
Paggi, Joseph M. ;
Park, Chanhee ;
Bennett, Christopher ;
Salzberg, Steven L. .
NATURE BIOTECHNOLOGY, 2019, 37 (08) :907-+
[4]   Initial sequencing and analysis of the human genome [J].
Lander, ES ;
Int Human Genome Sequencing Consortium ;
Linton, LM ;
Birren, B ;
Nusbaum, C ;
Zody, MC ;
Baldwin, J ;
Devon, K ;
Dewar, K ;
Doyle, M ;
FitzHugh, W ;
Funke, R ;
Gage, D ;
Harris, K ;
Heaford, A ;
Howland, J ;
Kann, L ;
Lehoczky, J ;
LeVine, R ;
McEwan, P ;
McKernan, K ;
Meldrim, J ;
Mesirov, JP ;
Miranda, C ;
Morris, W ;
Naylor, J ;
Raymond, C ;
Rosetti, M ;
Santos, R ;
Sheridan, A ;
Sougnez, C ;
Stange-Thomann, N ;
Stojanovic, N ;
Subramanian, A ;
Wyman, D ;
Rogers, J ;
Sulston, J ;
Ainscough, R ;
Beck, S ;
Bentley, D ;
Burton, J ;
Clee, C ;
Carter, N ;
Coulson, A ;
Deadman, R ;
Deloukas, P ;
Dunham, A ;
Dunham, I ;
Durbin, R ;
French, L .
NATURE, 2001, 409 (6822) :860-921
[5]   Genome graphs and the evolution of genome inference [J].
Paten, Benedict ;
Novak, Adam M. ;
Eizenga, Jordan M. ;
Garrison, Erik .
GENOME RESEARCH, 2017, 27 (05) :665-676
[6]   Fast and accurate genomic analyses using genome graphs [J].
Rakocevic, Goran ;
Semenyuk, Vladimir ;
Lee, Wan-Ping ;
Spencer, James ;
Browning, John ;
Johnson, Ivan J. ;
Arsenijevic, Vladan ;
Nadj, Jelena ;
Ghose, Kaushik ;
Suciu, Maria C. ;
Ji, Sun-Gou ;
Demir, Gulfem ;
Li, Lizao ;
Toptas, Berke C. ;
Dolgoborodov, Alexey ;
Pollex, Bjorn ;
Spulber, Iosif ;
Glotova, Irina ;
Komar, Peter ;
Stachyra, Andrew L. ;
Li, Yilong ;
Popovic, Milos ;
Kallberg, Morten ;
Jain, Amit ;
Kural, Deniz .
NATURE GENETICS, 2019, 51 (02) :354-+
[7]   Assembly of a pan-genome from deep sequencing of 910 humans of African descent [J].
Sherman, Rachel M. ;
Forman, Juliet ;
Antonescu, Valentin ;
Puiu, Daniela ;
Daya, Michelle ;
Rafaels, Nicholas ;
Boorgula, Meher Preethi ;
Chavan, Sameer ;
Vergara, Candelaria ;
Ortega, Victor E. ;
Levin, Albert M. ;
Eng, Celeste ;
Yazdanbakhsh, Maria ;
Wilson, James G. ;
Marrugo, Javier ;
Lange, Leslie A. ;
Williams, L. Keoki ;
Watson, Harold ;
Ware, Lorraine B. ;
Olopade, Christopher O. ;
Olopade, Olufunmilayo ;
Oliveira, Ricardo R. ;
Ober, Carole ;
Nicolae, Dan L. ;
Meyers, Deborah A. ;
Mayorga, Alvaro ;
Knight-Madden, Jennifer ;
Hartert, Tina ;
Hansel, Nadia N. ;
Foreman, Marilyn G. ;
Ford, Jean G. ;
Faruque, Mezbah U. ;
Dunston, Georgia M. ;
Caraballo, Luis ;
Burchard, Esteban G. ;
Bleecker, Eugene R. ;
Araujo, Maria I. ;
Herrera-Paz, Edwin F. ;
Campbell, Monica ;
Foster, Cassandra ;
Taub, Margaret A. ;
Beaty, Terri H. ;
Ruczinski, Ingo ;
Mathias, Rasika A. ;
Barnes, Kathleen C. ;
Salzberg, Steven L. .
NATURE GENETICS, 2019, 51 (01) :30-+
[8]   dbSNP: the NCBI database of genetic variation [J].
Sherry, ST ;
Ward, MH ;
Kholodov, M ;
Baker, J ;
Phan, L ;
Smigielski, EM ;
Sirotkin, K .
NUCLEIC ACIDS RESEARCH, 2001, 29 (01) :308-311
[9]   Long-read sequencing and de novo assembly of a Chinese genome [J].
Shi, Lingling ;
Guo, Yunfei ;
Dong, Chengliang ;
Huddleston, John ;
Yang, Hui ;
Han, Xiaolu ;
Fu, Aisi ;
Li, Quan ;
Li, Na ;
Gong, Siyi ;
Lintner, Katherine E. ;
Ding, Qiong ;
Wang, Zou ;
Hu, Jiang ;
Wang, Depeng ;
Wang, Feng ;
Wang, Lin ;
Lyon, Gholson J. ;
Guan, Yongtao ;
Shen, Yufeng ;
Evgrafov, Oleg V. ;
Knowles, James A. ;
Thibaud-Nissen, Francoise ;
Schneider, Valerie ;
Yu, Chack-Yung ;
Zhou, Libing ;
Eichler, Evan E. ;
So, Kwok-Fai ;
Wang, Kai .
NATURE COMMUNICATIONS, 2016, 7
[10]   One reference genome is not enough [J].
Yang, Xiaofei ;
Lee, Wan-Ping ;
Ye, Kai ;
Lee, Charles .
GENOME BIOLOGY, 2019, 20 (1)