Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics

被引：21

作者：

Menegaux, Romain ^{[1
,2
]}

Vert, Jean-Philippe ^{[1
,2
,3
,4
]}

机构：

[1] PSL Res Univ, MINES ParisTech, CBIO Ctr Computat Biol, Paris, France

[2] PSL Res Univ, Inst Curie, INSERM, U900, Paris, France

[3] PSL Res Univ, CNRS, Dept Math & Applicat, Ecole Normale Super, Paris, France

[4] Google Brain, 8 Rue Londres, F-75009 Paris, France

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 2019年 / 26卷 / 06期

关键词：

metagenomics; sequencing; classification; embedding; CLASSIFICATION;

D O I：

10.1089/cmb.2018.0174

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

We propose a new model for fast classification of DNA sequences output by next-generation sequencing machines. The model, which we call fastDNA, embeds DNA sequences in a vector space by learning continuous low-dimensional representations of the k-mers it contains. We show on metagenomics benchmarks that it outperforms the state-of-the-art methods in terms of accuracy and scalability.

引用

页码：509 / 518

页数：10

共 50 条

[21] NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model
Wei, Ze-Gang
Zhang, Shao-Wu
BMC BIOINFORMATICS, 2018, 19
[22] REMOVAL OF HOST DNA ENHANCES METAGENOMICS SEQUENCING SENSITIVITY OF THE MICROBIOTA IN TISSUE BIOPSIES
Cheng, Wing Yin
Liu, Weixin
Chu, Eagle S.
Wong, Sunny H.
Sung, Joseph J.
Yu, Jun
GASTROENTEROLOGY, 2021, 160 (06) : S732 - S733
[23] The integration of sequencing and bioinformatics in metagenomics
Firouz Abbasian
Robin Lockington
Mallavarapu Megharaj
Ravi Naidu
Reviews in Environmental Science and Bio/Technology, 2015, 14 : 357 - 383
[24] The integration of sequencing and bioinformatics in metagenomics
Abbasian, Firouz
Lockington, Robin
Megharaj, Mallavarapu
Naidu, Ravi
REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY, 2015, 14 (03) : 357 - 383
[25] Metagenomics uBiome: participative sequencing
不详
BIOFUTUR, 2013, (342) : 15 - 15
[26] Food authentication from shotgun sequencing reads with an application on high protein powders
Haiminen, Niina
Edlund, Stefan
Chambliss, David
Kunitomi, Mark
Weimer, Bart C.
Ganesan, Balasubramanian
Baker, Robert
Markwell, Peter
Davis, Matthew
Huang, B. Carol
Kong, Nguyet
Prill, Robert J.
Marlowe, Carl H.
Quintanar, Andre
Pierre, Sophie
Dubois, Geraud
Kaufman, James H.
Parida, Laxmi
Beck, Kristen L.
NPJ SCIENCE OF FOOD, 2019, 3 (01)
[27] Food authentication from shotgun sequencing reads with an application on high protein powders
Niina Haiminen
Stefan Edlund
David Chambliss
Mark Kunitomi
Bart C. Weimer
Balasubramanian Ganesan
Robert Baker
Peter Markwell
Matthew Davis
B. Carol Huang
Nguyet Kong
Robert J. Prill
Carl H. Marlowe
André Quintanar
Sophie Pierre
Geraud Dubois
James H. Kaufman
Laxmi Parida
Kristen L. Beck
npj Science of Food, 3
[28] Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases
Brown, Julianne R.
Bharucha, Tehmina
Breuer, Judith
JOURNAL OF INFECTION, 2018, 76 (03) : 225 - 240
[29] Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA
Costa, Lucas
Marques, Andre
Buddenhagen, Chris
Thomas, William Wayt
Huettel, Bruno
Schubert, Veit
Dodsworth, Steven
Houben, Andreas
Souza, Gustavo
Pedrosa-Harand, Andrea
ANNALS OF BOTANY, 2021, 128 (07) : 835 - 848
[30] Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, Heng
Ruan, Jue
Durbin, Richard
GENOME RESEARCH, 2008, 18 (11) : 1851 - 1858

← 1 2 3 4 5 →