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De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

D. Hernandez, P. Francois, L. Farinelli, M. Osteras, J. Schrenzel
2008 Genome Research  
We propose a de novo assembler software that is dedicated to process such data.  ...  The assembly results were validated by comparing data sets that were obtained experimentally for Staphylococcus aureus strain MW2 and Helicobacter acinonychis strain Sheeba with that of their published  ...  This example is one of the many that can be found in the overlap graph constructed from the Staphylococcus aureus strain MW2 reads data set.  ... 
doi:10.1101/gr.072033.107 pmid:18332092 pmcid:PMC2336802 fatcat:hkywtm7ggvdixojiys2k5o36ii

Characterizing Phage Genomes for Therapeutic Applications

Casandra Philipson, Logan Voegtly, Matthew Lueder, Kyle Long, Gregory Rice, Kenneth Frey, Biswajit Biswas, Regina Cer, Theron Hamilton, Kimberly Bishop-Lilly
2018 Viruses  
Essential analysis checkpoints and warnings are detailed for obtaining high-quality genomes, excluding undesirable candidates, rigorously assessing a phage genome for safety and evaluating sequencing contamination  ...  The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria.  ...  from Step 1 were subsampled then assembled de novo.  ... 
doi:10.3390/v10040188 pmid:29642590 pmcid:PMC5923482 fatcat:36uvchktg5byvjbe6kojq3kv5m

Completing Circular Bacterial Genomes With Assembly Complexity by Using a Sampling Strategy From a Single MinION Run With Barcoding

Yu-Chieh Liao, Hung-Wei Cheng, Han-Chieh Wu, Shu-Chen Kuo, Tsai-Ling Yang Lauderdale, Feng-Jui Chen
2019 Frontiers in Microbiology  
The Oxford Nanopore MinION is an affordable and portable DNA sequencer that can produce very long reads (tens of kilobase pairs), which enable de novo bacterial genome assembly.  ...  pittii, and Staphylococcus aureus.  ...  ACKNOWLEDGMENTS We would like to thank National Core Facility for Biopharmaceuticals (NCFB, MOST 106-2319-B-492-002) and National Center for High-performance Computing (NCHC) of National Applied Research  ... 
doi:10.3389/fmicb.2019.02068 pmid:31551994 pmcid:PMC6737777 fatcat:bqd5yfyg4baflirssqve3teq3a

Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains

Richard W. Davis, Andrew D. Brannen, Mohammad J. Hossain, Scott Monsma, Paul E. Bock, Matthias Nahrendorf, David Mead, Michael Lodes, Mark R. Liles, Peter Panizzi
2016 BMC Genomics  
Furthermore, we provide independent confirmation of our segmental arrangement of the Tager 104 genome by the sole use of Lucigen NxSeq libraries filled by paired-end MiSeq reads and alignment with SPAdes  ...  Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE).  ...  Support also provided by the National Institute of Allergy and Infectious Diseases grant 2R44AI085840-02 (to D.M., P.P. and M.R.L.).  ... 
doi:10.1186/s12864-016-2433-8 pmid:26940863 pmcid:PMC4778325 fatcat:jcb7c5s6ancgtgu2smxapdfrwq

A comparative evaluation of genome assembly reconciliation tools

Hind Alhakami, Hamid Mirebrahim, Stefano Lonardi
2017 Genome Biology  
In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.  ...  A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity.  ...  Acknowledgments We would like to thank Dr Alejandro Sanchez (National Autonomous University of Mexico), Dr Michael Schatz (Cold Spring Harbor Laboratory), and Dr Yu-Chieh Liao (National Health Research  ... 
doi:10.1186/s13059-017-1213-3 pmid:28521789 pmcid:PMC5436433 fatcat:fw75im4wrberjo4hmxlw7fzimi

Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40

Melanie Zischka, Carsten T Künne, Jochen Blom, Dominique Wobser, Türkân Sakιnç, Kerstin Schmidt-Hohagen, P Wojtek Dabrowski, Andreas Nitsche, Johannes Hübner, Torsten Hain, Trinad Chakraborty, Burkhard Linke (+20 others)
2015 BMC Genomics  
Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source.  ...  Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions  ...  Acknowledgements We would like to thank our cooperation partners for their support and fruitful discussions. A  ... 
doi:10.1186/s12864-015-1367-x pmid:25887115 pmcid:PMC4374294 fatcat:6agvtfkctvaipjhbjz2p2mi5nu

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

Henk C den Bakker, Craig A Cummings, Vania Ferreira, Paolo Vatta, Renato H Orsi, Lovorka Degoricija, Melissa Barker, Olga Petrauskene, Manohar R Furtado, Martin Wiedmann
2010 BMC Genomics  
genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome.  ...  Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main Listeria species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory  ...  Acknowledgements We would like to thank the JCVI for providing the JCVI Annotation Service, which provided us with automatic annotation data and the manual  ... 
doi:10.1186/1471-2164-11-688 pmid:21126366 pmcid:PMC3019230 fatcat:6nqy5qtgsjbd7jqyphlalxzv54

D3.8- Abstract book for 1st Annual Scientific Meeting (ASM) [article]

2021 Zenodo  
This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No 773830.  ...  This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No 773830.  ...  short and long reads.  ... 
doi:10.5281/zenodo.4897288 fatcat:b6t7jvr5q5fgrlzouppu6wdiym

Perfecting bacterial genome assembly

Rather, they produce fragmented and error-containing pieces of the genome (reads), and the computational task of reconstructing a genome from sequencing reads is known as assembly.  ...  In this thesis, I investigate the best practices for assembling bacterial genomes and develop new algorithms which address shortcomings of existing methods.  ...  Acknowledgements Acknowledgments We would like to thank Wendy Wilson for conducting the long-range PCR amplification.  ... 
doi:10.26180/19407284 fatcat:f4ufjawyw5fspgfybhikzl22ga

Resources for the analysis of bacterial and microbial genomic data with a focus on antibiotic resistance [article]

Valentina Galata, Universität Des Saarlandes
The analysis of this isolate collection allowed for the identification of bacterial species demonstrating increasing resistance rates, to construct species pan-genomes from the de novo assembled genomes  ...  This resource provides access to the resistance information and genomic data, and implements functionality to compare submitted genes or genomes to the data included in the resource.  ...  Funding Siemens Healthcare and in parts by the Best Ageing (grant number 306031) from the European Union.  ... 
doi:10.22028/d291-31414 fatcat:j2fwsqsp65aaxkdnvayyrwjw3e

ASPA 23rd Congress Book of Abstracts

Fulvia Bovera
2019 Italian Journal of Animal Science  
Aiming to a dietary pattern that achieves 5% to 6% of calories from SFA and considering a daily need of about 2000 kcal, no more than 100-120 kcal should come from SFA.  ...  Thus, one serving of meat (100 g) had 99.7 kcal of which only 9.9 kcal were from fat, that is only 9.9% of the total energy.  ...  by sequencing using 300 bp paired-end Illumina Miseq platform.  ... 
doi:10.1080/1828051x.2019.1622269 fatcat:7qufgthjzbggtcsbbxhge7ajgu

Genome and transcriptome architecture in Pyrococcus furiosus

Felix Grünberger
Additionally, we could prove that despite the relatively high abundance of insertion sequences in the 2 Mbp genome, the handling of a lab culture for [...]  ...  Here, we have primarily been interested in the genome and transcriptome architecture, the regulatory roles of transcription factors and post-transcriptional mechanisms in the hyperthermophilic model archaeon  ...  The authors thank Esther Schüler (DSMZ, Department Microorganisms) for providing biomass and Annett Bellack for providing genomic DNA from Pyrococcus furiosus.  ... 
doi:10.5283/epub.46432 fatcat:z7lsvm6qmrb2palsokhjhuwgw4

Abstract Session 01 – Cell Therapy: Immunotherapy

2011 Transfusion Medicine and Hemotherapy  
T cells generated from PBMCs of healthy donors by HSP70/PCs were analyzed for phenotype and function.  ...  Viral infections resulting from reactivation of latent viruses (e.g. CMV, ADV, EBV) are associated with high morbidity and mortality after transplantation.  ...  procedure was repeated every two weeks to exclude de-novo alloimmunization.  ... 
doi:10.1159/000333039 fatcat:czj2nomhrjghjcred6ilw2btdq

A computational biology approach to studying algae-bacterial interactions

Ulrich Johan Kudahl, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Alison G. Smith
I developed a genome scale metabolic model of metabolism of M. loti that enabled simulation of growth. The model simulates 1908 enzymatic reactions and takes 1804 metabolites into account.  ...  I have applied methods from the field of computational biology to study the interactions between these organisms and other similar partnerships, with the aim of uncovering new insights.  ...  Sequencing was set to generate 75 bp pair-end reads.  ... 
doi:10.17863/cam.24234 fatcat:d5xl4ncn45a7rilhvur3xle74m

Investigation of bacterial secondary metabolite pathways [article]

Alexander Von Tesmar, Universität Des Saarlandes, Universität Des Saarlandes
The microcins are attached to the C-terminal end of enterobactin and subsequently actively imported by other species in a "trojan horse" fashion. [64][65][66] Recent insights into the secondary metabolome  ...  Several compounds produced during respiratory tract infections are known to modulate the gene expression of the host cells, produce free radicals or scavenging iron from epithelial cells. 58, 59 The human  ...  We thank Kirsten Harmrolfs and Thomas Hoffmann for discussion and critical reading of the manuscript. We thank Silke Herok-Schoepper for technical assistance.  ... 
doi:10.22028/d291-26823 fatcat:l6nksumx7nh5npiqojkyscnnia
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