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Joseph Mitchell
Joseph Mitchell

Life On The Line Torrent

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

Life on the Line torrent

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The battle of the benchtop sequencers (between newcomer Ion Torrent, recently purchased for a staggering $725 million by Life Technologies, and the directly competing MiSeq instrument announced by established sequencing giant Illumina) has taken a turn for the surreal, with this YouTube ad by Ion Torrent following a well-trodden "Mac vs PC" line:

Torrent As blue as the ocean, an affordable sea fishing reel in five sizes covering all major types of angling. Built with an indestructible nylon housing and metal components for optimum power and long life. We are confident that this new model from Quantum US will be a popular best-seller for saltwater fishing in Europe.

Standard features:-2+1 ball bearings -Anodised aluminium spool -Continuous anti-reverse -S-curve line distribution -Robust nylon housing -Powerful multi-disc front drag system -CNC metal reel handle

This product is currently out of stock, please check our complete line of in-stock DNA Sequencers by clicking the orange link below or give one of the members of our sales team a call today at (860) 691-2213 so we can help you find a suitable replacement.

Last month's splendidly atmospheric description of making a study of life in torrents by William H. Amos, of Vermont, United States took me back to days foraging in the Dolomites of Northern Italy in the 80's and irregular visits to the Carpathians in the early 90's. It reminded me of the problems of collecting; particularly diatoms, and other algae in the flumes and their spray zones and in the moist overhangs of "Where Eagle's Dare" country.

The Torrent is equipped with eight underwing pylons which provide hardpoints for a wide variety of French bombs, missiles, fuel tanks, and other mounts. A single specialized weapon station under the main body allows the carrying of one angelfire hyperspatial missile. These systems have undergone numerous revisions and upgrades over the Torrent's lifetime.

Visit the state-of-the-art housing accommodations on GCU's beautiful campus from wherever you are in the world. These virtual tours provide 360-degree views, photo and information to help you choose the best on-campus housing for your lifestyle.

GCU's Department of Housing Operations manages the housing reservations and logistical needs of both the new and returning residential community on campus. Housing Operations oversees the planning of living area allocation and growth, the creation and maintenance of the online housing selection processes, as well as the communication and accountability of housing policies and deadlines.

Extraordinary Feel - This reel boasts an Accurate & effective 0-10 magnetic brake, providing the angler with on-the-fly tournament ready adjustments. Double line winding shafts increase the winding stability and durability.

Easy Maintenance - A unique screwed oil hole in the side-plate helps you quickly and efficiently lubricate in order to lengthen reel life and maximize performance. Novice and Pro anglers alike will benefit from this easy method, no more lost or broken parts for basic maintenance.

In these lines, the reader sees that Poe relates this trouble differently than those commonly plagued with gloom. This darker tone is a facet of his character. He was not as others were. He saw things in a much different light. Where averagely others saw passions and goodness in only the lighthearted things like spring, he saw the beauty of the dark and the peculiar.

Literature is the one art form that above all the others brings multiple people of different perspectives to the same table. Conversations begin and end with the beauty of this craft. For some, it can be a vehicle of life, a minister of a therapy that has no prescription drug form.

The effect of substituting Platinum HiFi PCR supermix with Kapa HiFi in the PGM library prep amplification step. A) The percentage of the P. falciparum genome covered at different read depths. The blue line shows the data obtained with the recommended Platinum enzyme and the green line with Kapa HiFi. The red line depicts ideal coverage behavior. B) The number of bases covered at different depths. C) Sequence representation vs. GC-content plots.

Illustration of platform-specific errors. The panels show Artemis BAM views with reads (horizontal bars) mapping to defined regions of chromosome 11 of P. falciparum from PacBio (P; top), Ion Torrent (I; middle) and MiSeq (M; bottom). Red vertical dashes are 1 base differences to the reference and white points are indels. A) Illustration of errors in Illumina data after a long homopolymer tract. Ion torrent data has a drop of coverage and multiple indels are visible in PacBio data. B) Example of errors associated with short homopolymer tracts. Multiple insertions are visible in the PacBio Data, deletions are observed in the PGM data and the MiSeq sequences read generally correct through the homopolymer tract. C) Example of strand specific deletions (red circles) observed in Ion Torrent data.

Accuracy of SNP detection from the S. aureus datasets generated from each platform, compared against the reference genome of its close relative S . aureus USA300_FPR3757. Both the Torrent server variant calling pipeline and SAMtools were used for Ion Torrent data; SAMtools was used for Illumina data and SMRT portal pipeline for PacBio data. A) The percentage of SNPs detected using each platform overall (blue bar), and outside of repeats, indels and mobile genetic elements (red bar). B) The number of incorrect SNP calls for each platform overall (blue bar), and outside of repeats, indels and mobile genetic elements (red bar).

Overall the rate of SNP calling was slightly higher for the Ion Torrent data than for Illumina data (chi square p value 3.15E-08), with approximately 82% of SNPs being correctly called for the PGM and 68-76% of the SNPs being detected from the Illumina data (Figure 5A). Conversely, the rate of false SNP calls was higher with Ion Torrent data than for Illumina data (Figure 5B). SNP calling from PacBio data proved more problematic, as existing tools are optimized for short-read data and not for high error-rate long-read data. We were reliant on SNPs called by the SMRT portal pipeline for this analysis. Our results showed that SNP detection from PacBio data was not as accurate as that from the other platforms, with overall only 71% of SNPs being detected and 2876 SNPs being falsely called (Additional file 5: Table S6).

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