Sequencing

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11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting EDGE V2.0: AN UPDATED OF THE EMPOWERING THE DEVELOPMENT OF GENOMICS EXPERTISE BIOINFORMATICS PLATFORM Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.11) Chien‐Chi Lo, Po‐E Li, Yan Xu, Sanaa Ahmed, Shihai Feng, Karen Davenport, Patrick Chain Los Alamos National Laboratory Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current public and private databases with raw data for genomes and metagenomes. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals that often require highly specialized data processing, the wide array of tools that individually perform only small fractions of any given analysis, the large number of software and hardware dependencies these tools require to function, and the detailed expertise required to perform and interpret these analyses. In 2015, to address many of these issues, we have developed an intuitive web‐based environment with a wide assortment of integrated and cutting‐edge bioinformatics tools1. These preconfigured workflows provide even novice next‐generation sequencing users with the ability to perform a number of complex analyses (e.g. metagenome analyses) with only a few mouse clicks, and, within the context of the same web environment, allow users to visualize and further interrogate the results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for researchers who lack dedicated bioinformatics resources. Using the same strategy we have now expanded EDGE with (i) an amplicon data analysis module, (ii) a specialty genes detection module (for antibiotic resistance genes and virulence genes), (iii) UGE cluster submission support, (iv) MEGAHIT metagenome assembler, (v) a secure user management system update, (vi) new GOTTCHA database integration, (vii) third‐ party tools upgrade, (viii) and more interactive features for the result page. The improved EDGE v2.0 widens the usage for the NGS data analysis. 1. http://biorxiv.org/content/early/2016/02/21/040477 45
11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting MOLECULAR DIVERSITY OF BRUCELLA STRAINS FROM THE COUNTRY OF GEORGIA Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.12) Keti Sidamonidze 1 , Kevin Drees 2 , Jeffrey Foster 2 , Ekaterine Zhgenti 1 , Tea Tevdoradze 1 , Nino Trapaidze 1 , Gvantsa Chanturia 1 , Paata Imnadze 1 , Mikeljon Nikolich 3 1 National Center for Disease Control and Public Health, Georgia, 2 University of New Hampshire, 3 Walter Reed Army Institute of Research Brucellosis is a globally important zoonotic disease that is endemic in the country of Georgia, where it causes substantial human morbidity and significant agricultural economic losses. Because of its high infectivity, Brucella abortus and B. melitensis are classified as Category B biological threat agents. Lack of genetic resolution with available methods has made it challenging to understand its evolutionary history and determine the spread of this pathogen across the globe. Whole genome sequencing (WGS) allows for a deeper understanding of phylogenetic relationships among bacterial strains. In order to assess genetic variation among Brucella spp. circulating in Georgia, 15 Brucella strains – B. melitensis (n=5) and B. abortus (n=10), were whole genome sequenced. These strains were chosen as representatives of major genetic clusters, previously determined by MLVA‐15 as part of the Defense Threat Reduction Agency’s Cooperative Biological Research project GG‐17. Whole genome assemblies from these strains were aligned to the reference genomes for each species, B. abortus‐ 2308 and B.melitensis‐16M, respectively, for SNP discovery. A phylogenetic comparison of Georgian Brucella whole genome sequences to a worldwide collection of genomes showed that Georgian strains of B. abortus largely form a unique clade basal to the most common radiation of strains from biovars 1, 2, and 4, and are most similar to strains from Central Asia. Georgian B. melitensis isolates are less distinct and appear to mostly fall into the East Mediterranean lineage, but in select cases, also group with isolates found worldwide. Based on these WGS data, 15 Brucella strains were chosen for MLST analysis using the online database: BrucellaBase: Genome Information Resource. This study revealed that Brucella strains belong to sequence type 2 and 8 (ST2 and ST8). This panel will allow the screening of not only additional archival isolates, but also newly isolated Brucella strains in Georgia and the Caucasus region, thus allowing for a rapid assessment of their global phylogenetic context. 46
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Reliable solutions for focused NGS
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