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https://www.readbyqxmd.com/read/28794860/minion-analysis-and-reference-consortium-phase-2-data-release-and-analysis-of-r9-0-chemistry
#1
Miten Jain, John R Tyson, Matthew Loose, Camilla L C Ip, David A Eccles, Justin O'Grady, Sunir Malla, Richard M Leggett, Ola Wallerman, Hans J Jansen, Vadim Zalunin, Ewan Birney, Bonnie L Brown, Terrance P Snutch, Hugh E Olsen
BACKGROUND: Long-read sequencing is rapidly evolving and reshaping the suite of opportunities for genomic analysis. For the MinION in particular, as both the platform and chemistry develop, the user community requires reference data to set performance expectations and maximally exploit third-generation sequencing. We performed an analysis of MinION data derived from whole genome sequencing of Escherichiacoli K-12 using the R9.0 chemistry, comparing the results with the older R7.3 chemistry...
2017: F1000Research
https://www.readbyqxmd.com/read/28794062/high-quality-de-novo-genome-assembly-of-the-dekkera-bruxellensis-yeast-isolate-using-nanopore-minion-sequencing
#2
Téo Fournier, Jean-Sébastien Gounot, Kelle Freel, Corinne Cruaud, Arnaud Lemainque, Jean-Marc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich
Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is to obtain the complete sequence and high quality assembly of a reference genome...
August 9, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28775309/rapid-de-novo-assembly-of-the-european-eel-genome-from-nanopore-sequencing-reads
#3
Hans J Jansen, Michael Liem, Susanne A Jong-Raadsen, Sylvie Dufour, Finn-Arne Weltzien, William Swinkels, Alex Koelewijn, Arjan P Palstra, Bernd Pelster, Herman P Spaink, Guido E van den Thillart, Ron P Dirks, Christiaan V Henkel
We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU. The resulting genome assembly significantly improves on a previous draft based on short reads only, both in terms of contiguity (N50 1.2 Mbp) and structural quality. This combination of affordable nanopore sequencing and light weight assembly promises to make high-quality genomic resources accessible for many non-model plants and animals...
August 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28774990/complete-genome-sequence-of-achromobacter-denitrificans-pr1
#4
Ana C Reis, Kevin Kroll, Margarita Gomila, Boris A Kolvenbach, Philippe F X Corvini, Olga C Nunes
Achromobacter denitrificans strain PR1 was isolated from an enrichment culture able to use sulfamethoxazole as an energy source. Here, we describe the complete genome of this strain sequenced by Illumina MiSeq and Oxford Nanopore MinION.
August 3, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28747151/comparative-analysis-of-targeted-long-read-sequencing-approaches-for-characterization-of-a-plant-s-immune-receptor-repertoire
#5
Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D G Jones, Matthew D Clark
BACKGROUND: The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified...
July 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28722025/nanopore-long-read-rnaseq-reveals-widespread-transcriptional-variation-among-the-surface-receptors-of-individual-b-cells
#6
Ashley Byrne, Anna E Beaudin, Hugh E Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M DuBois, E Camilla Forsberg, Mark Akeson, Christopher Vollmers
Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification...
July 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28720805/a-portable-system-for-rapid-bacterial-composition-analysis-using-a-nanopore-based-sequencer-and-laptop-computer
#7
Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema, for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all 20 of the bacterial species present in the mock bacterial community...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717043/tandem-amplification-of-sccmec-can-drive-high-level-methicillin-resistance-in-mrsa
#8
Laura A Gallagher, Simone Coughlan, Nikki S Black, Pierce Lalor, Elaine M Waters, Bryan Wee, Mick Watson, Tim Downing, J Ross Fitzgerald, Gerard T A Fleming, James P O'Gara
Hospital-associated methicillin-resistant Staphylococcus aureus strains typically express high level, homogenous (HoR) β-lactam resistance, whereas community-associated MRSA (CA-MRSA) more commonly express low level heterogeneous (HeR) resistance. Expression of the HoR phenotype typically requires both increased expression of the mecA gene, carried on the Staphylococcus cassette chromosome SCCmec element, and additional mutational event(s) elsewhere on the chromosome. Here the oxacillin concentration in a chemostat culture of the CA-MRSA strain USA300 was increased from 8 μg/ml to 130 μg/ml over 13 days to isolate highly oxacillin resistant derivatives...
July 17, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28715998/detection-of-active-transposable-elements-in-arabidopsis-thaliana-using-oxford-nanopore-sequencing-technology
#9
Emilie Debladis, Christel Llauro, Marie-Christine Carpentier, Marie Mirouze, Olivier Panaud
BACKGROUND: Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV)...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28696556/1d-genome-sequencing-on-the-oxford-nanopore-minion
#10
Sara Goodwin, Robert Wappel, W Richard McCombie
Today's short-read sequencing instruments can generate read lengths between 50 bp and 700 bp depending on the specific instrument. These high-throughput sequencing approaches have revolutionized genomic science, allowing hundreds of thousands of full genomes to be sequenced, and have become indispensable tools for many researchers. With greater insight has come the revelation that many genomes are much more complicated than originally thought and include many rearrangements and copy-number variations. Unfortunately, short-read sequencing technologies are not well suited for identifying many of these types of events...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28663031/mutational-analysis-in-bcr-abl1-positive-leukemia-by-deep-sequencing-based-on-nanopore-minion-technology
#11
Crescenzio F Minervini, Cosimo Cumbo, Paola Orsini, Luisa Anelli, Antonella Zagaria, Luciana Impera, Nicoletta Coccaro, Claudia Brunetti, Angela Minervini, Paola Casieri, Giuseppina Tota, Antonella Russo Rossi, Giorgina Specchia, Francesco Albano
We report a third-generation sequencing assay on nanopore technology (MinION) for detecting BCR-ABL1 KD mutations and compare the results to a Sanger sequencing(SS)-based test in 24 Philadelphia-positive (Ph+) leukemia cases. Our data indicates that MinION is markedly superior to SS in terms of sensitivity, costs and timesaving, and has the added advantage of determining the clonal configuration of multiple mutations. We demonstrate that MinION is suitable for employment in the hematology laboratory for detecting BCR-ABL1 KD mutation in Ph+ leukemias...
June 27, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28638050/de-novo-yeast-genome-assemblies-from-minion-pacbio-and-miseq-platforms
#12
Francesca Giordano, Louise Aigrain, Michael A Quail, Paul Coupland, James K Bonfield, Robert M Davies, German Tischler, David K Jackson, Thomas M Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Ning
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs. Compared with short reads, the assemblies obtained from long-read sequencing platforms have much higher contig continuity and genome completeness as long fragments are able to extend paths into problematic or repetitive regions. Many successful assembly applications of the Pacific Biosciences technology have been reported ranging from small bacterial genomes to large plant and animal genomes...
June 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#13
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28605506/multi-locus-and-long-amplicon-sequencing-approach-to-study-microbial-diversity-at-species-level-using-the-miniontm-portable-nanopore-sequencer
#14
Alfonso Benítez-Páez, Yolanda Sanz
Background: The miniaturised and portable DNA sequencer MinION TM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity. In this study, we tested the ability of the MinION TM platform to perform long amplicon sequencing in order to design new approaches to study microbial diversity using a multi-locus approach. Results: After compiling a robust database by parsing and extracting the rrn bacterial region from more than 67,000 complete or draft bacterial genomes, we demonstrated that the data obtained during sequencing of the long amplicon in the MinION TM device using R9 and R9...
June 12, 2017: GigaScience
https://www.readbyqxmd.com/read/28582401/deepnano-deep-recurrent-neural-networks-for-base-calling-in-minion-nanopore-reads
#15
Vladimír Boža, Broňa Brejová, Tomáš Vinař
The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp were reported); however it suffers from high sequencing error rate. We present an open-source DNA base caller based on deep recurrent neural networks and show that the accuracy of base calling is much dependent on the underlying software and can be improved by considering modern machine learning methods. By employing carefully crafted recurrent neural networks, our tool significantly improves base calling accuracy on data from R7...
2017: PloS One
https://www.readbyqxmd.com/read/28569745/the-microprotein-minion-controls-cell-fusion-and-muscle-formation
#16
Qiao Zhang, Ajay A Vashisht, Jason O'Rourke, Stéphane Y Corbel, Rita Moran, Angelica Romero, Loren Miraglia, Jia Zhang, Eric Durrant, Christian Schmedt, Srinath C Sampath, Srihari C Sampath
Although recent evidence has pointed to the existence of small open reading frame (smORF)-encoded microproteins in mammals, their function remains to be determined. Skeletal muscle development requires fusion of mononuclear progenitors to form multinucleated myotubes, a critical but poorly understood process. Here we report the identification of Minion (microprotein inducer of fusion), a smORF encoding an essential skeletal muscle specific microprotein. Myogenic progenitors lacking Minion differentiate normally but fail to form syncytial myotubes, and Minion-deficient mice die perinatally and demonstrate a marked reduction in fused muscle fibres...
June 1, 2017: Nature Communications
https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#17
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28503666/robust-long-read-native-dna-sequencing-using-the-ont-csgg-nanopore-system
#18
Jean-Michel Carter, Shobbir Hussain
Background: The ability to obtain long read lengths during DNA sequencing has several potentially important practical applications. Especially long read lengths have been reported using the Nanopore sequencing method, currently commercially available from Oxford Nanopore Technologies (ONT). However, early reports have demonstrated only limited levels of combined throughput and sequence accuracy. Recently, ONT released a new CsgG pore sequencing system as well as a 250b/s translocation chemistry with potential for improvements...
April 6, 2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28491281/annotated-mitochondrial-genome-with-nanopore-r9-signal-for-nippostrongylus-brasiliensis
#19
Jodie Chandler, Mali Camberis, Tiffany Bouchery, Mark Blaxter, Graham Le Gros, David A Eccles
Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response. The current reference genome for this parasite is highly fragmented with minimal annotation, but new advances in long-read sequencing suggest that a more complete and annotated assembly should be an achievable goal. We de-novo assembled a single contig mitochondrial genome from N. brasiliensis using MinION R9 nanopore data...
2017: F1000Research
https://www.readbyqxmd.com/read/28488487/too-much-direction
#20
Malcolm Harrison
So NHS England is to employ two more directors of nursing (news, 26 April). Presumably this will require the employment of at least two more admin staff and minions. Total cost? About £200,000 a year? Or about six or seven nurses, just the amount most wards seem to be short of.
May 10, 2017: Nursing Standard
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