An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.
An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes.
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DOI：
10.1186/s13059-021-02536-3
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发表时间：
2021-12-21
期刊：
影响因子：
12.3
通讯作者：
10KSG consortium
中科院分区：
文献类型：
--
作者：
Perez-Sepulveda BM;Heavens D;Pulford CV;Predeus AV;Low R;Webster H;Dykes GF;Schudoma C;Rowe W;Lipscombe J;Watkins C;Kumwenda B;Shearer N;Costigan K;Baker KS;Feasey NA;Hinton JCD;Hall N;10KSG consortium
我们开发了一种高效且廉价的管道，用于简化细菌分离株的大规模收集和基因组测序。该方法的评价涉及全球范围内的研究合作，重点是模式生物肠道沙门氏菌，10 KSG财团。在优化物流管道（包括在环境条件下将分离株作为治疗剂运输）后，该项目收集了来自低收入和中等收入国家的10，419株分离株。使用LITE pipeline进行文库构建，每个基因组的总试剂成本低于10美元。我们的方法可以应用于其他大型细菌收集，以支持全球合作。在线版本包含补充材料，可通过10.1186/s13059-021-02536-3获得。
We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. Following the optimization of a logistics pipeline that involved shipping isolates as thermolysates in ambient conditions, the project assembled a diverse collection of 10,419 isolates from low- and middle-income countries. The genomes were sequenced using the LITE pipeline for library construction, with a total reagent cost of less than USD$10 per genome. Our method can be applied to other large bacterial collections to underpin global collaborations. The online version contains supplementary material available at 10.1186/s13059-021-02536-3.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
15.8
作者：
Havelaar AH;Kirk MD;Torgerson PR;Gibb HJ;Hald T;Lake RJ;Praet N;Bellinger DC;de Silva NR;Gargouri N;Speybroeck N;Cawthorne A;Mathers C;Stein C;Angulo FJ;Devleesschauwer B;World Health Organization Foodborne Disease Burden Epidemiology Reference Group
通讯作者：
World Health Organization Foodborne Disease Burden Epidemiology Reference Group
DOI：
10.1056/nejmoa1800474
发表时间：
2018-10-11
期刊：
The New England journal of medicine
影响因子：
--
作者：
CRyPTIC Consortium and the 100,000 Genomes Project;Allix-Béguec C;Arandjelovic I;Bi L;Beckert P;Bonnet M;Bradley P;Cabibbe AM;Cancino-Muñoz I;Caulfield MJ;Chaiprasert A;Cirillo DM;Clifton DA;Comas I;Crook DW;De Filippo MR;de Neeling H;Diel R;Drobniewski FA;Faksri K;Farhat MR;Fleming J;Fowler P;Fowler TA;Gao Q;Gardy J;Gascoyne-Binzi D;Gibertoni-Cruz AL;Gil-Brusola A;Golubchik T;Gonzalo X;Grandjean L;He G;Guthrie JL;Hoosdally S;Hunt M;Iqbal Z;Ismail N;Johnston J;Khanzada FM;Khor CC;Kohl TA;Kong C;Lipworth S;Liu Q;Maphalala G;Martinez E;Mathys V;Merker M;Miotto P;Mistry N;Moore DAJ;Murray M;Niemann S;Omar SV;Ong RT;Peto TEA;Posey JE;Prammananan T;Pym A;Rodrigues C;Rodrigues M;Rodwell T;Rossolini GM;Sánchez Padilla E;Schito M;Shen X;Shendure J;Sintchenko V;Sloutsky A;Smith EG;Snyder M;Soetaert K;Starks AM;Supply P;Suriyapol P;Tahseen S;Tang P;Teo YY;Thuong TNT;Thwaites G;Tortoli E;van Soolingen D;Walker AS;Walker TM;Wilcox M;Wilson DJ;Wyllie D;Yang Y;Zhang H;Zhao Y;Zhu B
通讯作者：
Zhu B
影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.