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Microbiome | Full text | An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

To take advantage of affordable high-throughput next-generation sequencing technologies to characterize microbial community composition often requires the development of improved methods to overcome technical limitations inherent to the sequencing...
Mel Melendrez-Vallard's insight:

Insight from @patschloss via twitter sharing of this paper:

(i) They don't report error rates

(ii) They do N-stitching


I'd noticed the lack of error rates but not the stitching... A better paper released on this method in 2013 is: http://aem.asm.org/content/79/17/5112.full.pdf+html

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Tools and tips for scientific tinkers and tailors
Next gen sequencing, bioinformatics, virology, microbiology, genomes, zoonoses, workshops, conferences, all-around science geekery
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Sequencing Ebola in the field: a tale of nanopores, mosquitos and whatsapp

Posted on behalf of Lauren -------------------------------------------------- Since the 2nd of June I have been in Guinea contributing to the Ebola response by sequencing the new cases on the MinIO...
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Where do these 'primary' MERS cases come from?

I was just dropping by the General Directorate for Infection Prevention and Control's Middle East respiratory syndrome (MERS) statistics website ([1]; Kingdom of Saudi Arabia) and noticed this graph which I've snipped and labelled below.
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The Diversity and Geographical Structure of Orientia tsutsugamushi Strains from Scrub Typhus Patients in Laos

by Rattanaphone Phetsouvanh, Piengchan Sonthayanon, Sasithon Pukrittayakamee, Daniel H. Paris, Paul N. Newton, Edward J. Feil, Nicholas P. J.
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Guinea Ebola Ring Vaccination Trial Extended to Sierra Leone

Detection of a new case of Ebola virus disease in Kambia, Sierra Leone after the country had marked almost three weeks of zero cases has set in motion the first ‘ring vaccination’ use of the experimental Ebola vaccine in Sierra Leone, reports the...
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Evaluation of candidate vaccine approaches for MERS-CoV - Nature.com

Nature.com Evaluation of candidate vaccine approaches for MERS-CoV Nature.com The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) as a cause of severe respiratory disease highlights the need for effective approaches to CoV...
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Rapid host switching in generalist Campylobacter strains erodes the signal for ... - Nature.com

Rapid host switching in generalist Campylobacter strains erodes the signal for ... - Nature.com | Tools and tips for scientific tinkers and tailors | Scoop.it
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in...
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50-plus years of fungal viruses

50-plus years of fungal viruses | Tools and tips for scientific tinkers and tailors | Scoop.it

Highlights
• Historical perspective of fungal virus research.
• Description, classification and diversity of fungal virus families.
• Structural features of fungal virus particles.
• Hypovirulence and exploitation of mycoviruses in biological control of plant pathogenic fungi.


Via Steve Marek, Niklaus Grunwald, Chris Upton + helpers
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Avian Flu Diary: NEJM: Ebola in the United States — Public Reactions and Implications

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Omics! Omics!: The Road to Hell is Paved with Bioinformatics Formats

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Oscope – transcriptional dynamics of oscillating genes in single-cell RNA-Seq data | RNA-Seq Blog

Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. Researchers at the University
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TWiV 351: The dengue code

TWiV 351: The dengue code | Tools and tips for scientific tinkers and tailors | Scoop.it
Novel poxvirus isolate from an immunosuppressed patient, H1N1 and the gain-of-function debate, and attenuation of dengue virus by recoding the genome
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Novel DNA Vaccine Provides Protection Against MERS Virus

MedicalResearch.com Interview with: David B. Weiner, Ph.D. Professor, Department of Pathology and Laboratory Medicine Chair, Gene Therapy and Vaccine Program, CAMB Co-Leader Tumor Virology Program, Abramson Cancer Program University of Pennsylvania, Perelman School of Medicine Medical Resea...
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Active learning strategies for bioinformatics teaching

The more I read about how active learning techniques improve student learning, the more I am inclined to try out such techniques in my own teaching and training.
I attended the third week of Titus Brown’s “NGS Analysis Workshop”.
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The effects of demographic change on disease transmission and vaccine impact in a household structured population

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Interesting and important new paper: Microbial composition of purified waters 

Interesting and important new paper: Microbial composition of purified waters  | Tools and tips for scientific tinkers and tailors | Scoop.it
There is an interesting and potentially important new paper out from Caitlin Proctor, Marc Edwards and Amy Pruden: Microbial composition of purified waters and implications for regrowth control in municipal water systems in Environmental Science:...
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Hepatitis A-Like Virus Identified in Seals - Infection Control Today

Scientists in the Center for Infection and Immunity at Columbia University's Mailman School of Public Health have discovered a new virus in seals that is the closest known relative of the human hepatitis A virus.
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Evolutionary Relationship Between Existing Virus Families Mapped Out in a New ... - Scicasts (press release) (blog)

Evolutionary Relationship Between Existing Virus Families Mapped Out in a New ... - Scicasts (press release) (blog) | Tools and tips for scientific tinkers and tailors | Scoop.it
Oak Ridge, TN (Scicasts) — An Oak Ridge National Laboratory team of comparative genomics and computational science researchers compared approximately 4,000 complete virus genomes downloaded from a public database known as GenBank.
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Rescooped by Mel Melendrez-Vallard from Virology and Bioinformatics from Virology.ca
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Sierra Leone News : Ebola Breaks Out in a Remote Tonko Limba Village: Sierra Leone News


Via Ian M Mackay, PhD, Chris Upton + helpers
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CoreGenomics: S is for Sequencer: the new instrument from Ion Torrent

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Avian Flu Diary: ECDC Rapid Risk Assessment On MERS-CoV – August 28th

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40 reasons why you should blog about your research

It helps you become more clear about your ideas. It gives you practice at presenting your ideas for a non-specialist audience. It increases your visibility within academia. It increases your visibi...
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Simple & elegant solution to a big problem in DNA based microbial diversity studies

Simple & elegant solution to a big problem in DNA based microbial diversity studies | Tools and tips for scientific tinkers and tailors | Scoop.it
A new preprint has come out in PeerJ that presents a simple yet elegant solution to one of the bigger problems in DNA based microbial diversity studies.  The authors (Wenke Smets, Jonathan W Leff, ...
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Assembling B fragilis from MinION and Illumina data

You may have seen our bioRxiv preprint about the sequencing and assembly of B fragilis using Illumina + MinION sequence data.  Well, here is how to do it yourself. First get the data: # MinION data...
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The identification and characterization of novel transcripts from RNA-seq data

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