DNA Sequencing

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Ion Torrent
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A first peek at data from an Ion 316 chip Ion Torrent has made available an E.coli DH10B fragment dataset for the 316 chip, which is expected to be generally available early next month. I've theoretically had access to the data since Saturday, but a series of events (computer-free weekend, a crashed home computer, a personal day & a good but unbloggable conference) have meant that ambitious plans to analyze it are still in progress. So, what I discuss below is either from Ion's provided information or other sources, so take it with appropriate caution. The first statistic of note is that their dataset has 1.69M reads, with 1.53M of those >=50 bp long and 1.07M 100bp or longer. No enormous gains in read length in this dataset, though the curve might be shifted towards longer (one of the many analyses still being done). Now, the question immediately arises as to how typical this run is; their public dataset from the prior 314 chip with >400K reads is clearly an outlier A first peek at data from an Ion 316 chip
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Ion Community Home: Home Ion Community Home: Home 26 June 2013 Life Technologies Corporation organizational announcement, Read more at Note to Ion Torrent Customers, 26 June 2013 29 April 2013 "We did our diligence on Ion Torrent, we felt very good about the growth that it's getting in the technology and we are excited about having that as part of the portfolio." "I had a chance to meet the team recently and you can't leave Connecticut not coming away, really passionate about the mission there."
Ion OneTouch Ion Torrent™ Technology directly translates chemically encoded information (A, C, G, T) into digital information (0, 1) on a semiconductor chip. This approach marries simple chemistry to proprietary semiconductor technology—it's Watson meets Moore. The result is a sequencing technology that is simpler, faster, and more cost effective and scalable than any other next-generation sequencing technology available. SOLiD® next-generation sequencing > For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Ion OneTouch
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Homopolymer tails homopolymer tails a segment containing several of the same kind of deoxyribonucleotides arranged in tandem at the 3′ end of a DNA strand. See Appen- dix C, 1972, Lobban and Kaiser; terminal transferase. Homo sapiens the species to which human beings belong. The scientific name was coined in 1758 by Linnaeus. The estimated genome size is 3.2 × 109 base pairs. Homopolymer tails | Kickoff Homopolymer tails | Kickoff
An integrated semiconductor device enabling non-optical genome sequencing : Nature
IonTorrent: Benchtop Sequencing, Streamlined | MassGenomics New, smaller sequencing instruments are finding niches everywhere. Earlier this year in Less Is More: Sequencing on the Benchtop, I profiled three pint-sized sequencing instruments designed for next-gen sequencing on the benchtop: IonTorrent’s PGM, the Illumina MiSeq, and 454′s GS Junior. I must admit that I’m most intrigued by the PGM, probably because the idea of semiconductor sequencing is just so fascinating. One concern that I’ve heard about the PGM, however, was sample preparation. The time requirement and difficulty of sample prep was an immediate question at AGBT when Jonathan Rothberg first presented the instrument. IonTorrent: Benchtop Sequencing, Streamlined | MassGenomics
First Look: Data from IonTorrent’s 316 Chip | MassGenomics First Look: Data from IonTorrent’s 316 Chip | MassGenomics I got an early look at data from IonTorrent’s forthcoming semiconductor sequencing chip, called the 316. The data comes from a single sequencing run of E. coli, specifically the laboratory reference strain DH10B, not to be confused with the hybrid E. coli strain in the European outbreak that IonTorrent sequenced earlier this year. According to the run report, some 1.69 million reads were generated, of which 1.35 million were 100 base pairs or longer. It’s a nice, shiny report with color images, and of course I summarily ignored it in favor of looking at the data myself. The data package included an SFF file, a data format often used for Roche/454 data that contains read sequences and base qualities. There was also a BAM file, which included the read sequences aligned to the E. coli reference, indexed for random access.
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Escherichia coli O104:H4 str. TY-2482, whole genom... - Nucleotide result <p class="nojs"><strong>Warning:</strong> The NCBI web site requires JavaScript to function. <a href="http://www.ncbi.nlm.nih.gov/corehtml/query/static/unsupported-browser.html#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a></p> Escherichia coli O104:H4 str. TY-2482, whole genom... - Nucleotide result
Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology
Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4
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