In an online presentation, illumina emphasized the higher throughput and accuracy of its system compared to the ion torrent 314 chip. Here we compare the performances of two common benchtop sequencing platforms, illumina miseq and ion torrent personal genome machine pgm, for bacterial community profiling by 16s rrna v1v2 amplicon sequencing. Two of the most common sequencing platforms are the illumina miseq and the thermofisher ion torrent. Ion torrent launches attack ad against illuminas miseq.
While the technology is meant to directly rival illuminas sbs, ion sequencing has found a niche in smaller markets with players looking to sequence specific segments of a genome instead of its whole. Sequence quality parameters were determined for all data sets and centrally compared between laboratories. I want to lookup the gene expression btw these groups, compared with. Moreover, the false positive rate of base calling from ion torrent platform is still higher.
The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011. Next generation sequencing ngs technology has revolutionized genomic and genetic research. Comparative analysis of illumina and ion torrent high. The reversible terminated chemistry concept was invented by bruno canard and simon sarfati at the pasteur institute in paris. Illumina benchtop sequencing consumables are single cartridgebased with a separate flow cell. Comparison of illumina miseq, ion torrent pgm, 454 gs junior. The pgm and s5 reads are about 100 bp longer than the longest illumina reads. A comparison of illumina and ion torrent sequencing platforms. They showed that there still seems to be a problem with ion torrent pgm platform when they sequence plasmodium genome.
Illumina offers a variety of kit sizes ranging from a 50cycle kit to a 600cycle kit. Computational biologist mauricio carneiro, phd, describes a broad institute technology comparison to determine how pacific biosciences, ion torrent. Jul 17, 2019 nextgeneration sequencing is a powerful tool for virological surveillance. Life technologies, meantime, contests some of illumina s claims, touting the ion torrent platform as being a truly disruptive technology. Germanwide interlaboratory study compares consistency. While illumina and ion torrent sequencing platforms are used extensively for generating viral rna genome sequences, there is limited data comparing different platforms. Apr 22, 2012 nick talks about the new batch of laserprinter sized personal sequencing machines. Illumina will sell the product directly to its customers under the name ampliseq for illumina. Ion torrent library construction and template prep 90 minutes nextera sample prep.
Ion torrent, a division of thermofisher, has several sequencers, including the pgm and proton, which are based on detecting electrical signals from dna samples on a semiconductor chip. Illumina chemistry sequences homopolymers accurately, while ion torrent technology has an inherent problem in reading through homopolymers, as do all pyrosequencingbased technologies. Performance comparison between rapid sequencing platforms for ultralow coverage sequencing strategy. The second half is an explicit comparison against the available ion torrent. Aug 10, 2017 though illumina has largely dominated the rnaseq field, the simultaneous availability of ion torrent has left scientists wondering which platform is most effective for differential gene expression dge analysis. A comparison of illumina and ion torrent sequencing. Products include template and library prep, sequencing, analysis, and reporting. Higher cost per mb of data than most illumina instruments. The wellcome trust sanger institute, uk, recently published a comparison of the ion torrent pgm, illumina miseq, and pacific biosciences pacbio rs. The big surprise was illumina launching miseq, which radically lowered the entry point for the already dominant illumina platform. Ion torrent reads have variable lengths due to homopolymers and the correspondence of flow order to sequence if the flow order was a,t,c,g and the sequence of two fragments atcg and gcta, the former will read in all four flows but the latter only in the fourth flow. Jun 16, 20 quail, et al took a look at three platform in their paper.
The miseq system can go from dna to data in just over 8 hours. Accordingly, the illumina miseq and ion torrent personal genome machine. Illumina reads in a run will all have the same untrimmed length. Illumina sequencing versus other sequencing methods. The ion torrent proton compared to the illumina hiseq 2500 8. Mar 27, 2014 a recent plos one paper is perhaps the latest battle in the illumina vs lifetech war. My team uses an illumina miseq for targeted amplicon sequencing of cancer samples. How low can the price of a next generation dna sequencer go. In order to make the comparison fair, the authors should have used ion torrent 100 bp pe vs miseqs 150 bp pe reads, or ion torrent 100 bp vs miseq. Nextgeneration sequencing technologies and their application to. Miseq reagent kit v3 is available in sizes of 150 cycles and 600 cycles. The much simpler to use template chemistry for illumina has proven very popular versus emulsion pcr for ion torrent.
Comparison of illumina miseq and ion torrent pgm for nextgeneration sequencing of rna viruses abstract nextgeneration sequencing ngs technology is becoming a powerful tool in a public health setting for virus surveillance. Quantitative sequencing approaches make use of benchtop sequencers e. Performance comparison of benchtop highthroughput sequencing platforms nature biotech there is a rebuttal from iontorrent, the analysis section is not as much a rebuttal they are instead saying that the new kits are a lot better. Nextgen semiconductor sequencing workflow thermo fisher. For the ion torrent pgm platform against the illumina miseq platform, a bit of a marketing war has erupted, with both sides trading barbs. Lowdiversity sequencing on the illumina miseq platform. Although they have only looked at microbial genome with variable gcat content.
Pdf comparison of illumina miseq and the ion torrent pgm. What is the difference between solid, 454, and illumina. With the miseq system you can access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. Jul 30, 2012 comparing the performance of three nextgen sequencers. Should i use miseq or hiseq to generate data for assembling. Ion torrent pgm vs illumina miseq, ramujana, ion torrent, 121, 01052016 09. For the ion torrent pgm platform against the illumina miseq platform, a bit of a marketing war has erupted, with both sides. I have already used ion torrent pgm for sequencing but it only yielded about 23x coverage and around 4m usable reads size select. Thermos hydrogenion reading machines, known for speedier sequencing, have a more attractive price tag. Comparison of illumina miseq and ion torrent pgm for nextgeneration sequencing of rna viruses abstract. Different types of dna sequencing and analysis methods. Previous investigations of this question have typically used reference samples derived from cell lines and brain tissue, and do not involve biological variability. Under the ion torrent brand, applied biosystems produces four nextgeneration sequencers. The illumina miseq outputs significantly fewer reads table 1, but its read lengths are significantly longer, making it ideal for small genomes, sequencing long variable domains or targeted regions within a genome.
The miseq reagent kit v2 is available in sizes of 50 cycles, 300 cycles, and 500 cycles. By aligning both real and simulated illumina and ion torrent data with the twelve. We evaluated the illumina miseq, ion torrent pgm and ion torrent s5 platforms using a panel of sixteen specimens containing picornaviruses and. The ion pgm ion torrent, is ideal for amplicons, small.
Illumina sequencing platforms our innovative nextgeneration sequencing ngs platforms deliver exceptional data quality and accuracy, at a massive scale. Transitioning from ion torrent to illumina ngs platforms. Online illumina sequencing courses are free, interactive, and available any time. But illumina has plenty of competition in the contest for accurate, fast and cheap sequencing. Our starting point is a set of illuminasequenced pairedend fastq files that have been split or demultiplexed by sample and from which the barcodesadapters have already been removed. Which one would you recommend illumina miseq or ion torrent pgm. Thermo fisher will continue to sell ion ampliseq chemistry for both ivd and ruo applications to ion torrent ngs customers, and retains the right to make the technology available on. Comparison of ion torrent, pacific biosciences and. An intuitive touch screen and plugandplay reagents with rfid tracking add convenience. Here we compare the results obtained with those platforms to the performance of the illumina hiseq, the.
Nov 25, 20 this feature is not available right now. Jun 24, 2011 illumina has released a miseq dataset for li mg1655 on its website. Ive started teaching myself about nextgeneration sequencing in preparation for a new job, and im wondering what the main differences are between the 454, solid, and illuminasolexa machines, in terms of samplelibrary preparation and chemistry. Comparison of illumina miseq and ion torrent pgm for next. But they found that there were key differences in data quality of the platforms. In illumina data all sequence reads generated during a single experiment have the same lengths, while the lengths of ion torrent reads vary. Thermo fisher scientific and illumina sign agreement to. Here we perform the first reported study comparing both amplicon and shotgun sequencing for the three leading nextgeneration sequencing technologies. Jul 24, 2012 next generation sequencing ngs technology has revolutionized genomic and genetic research. The miseq system eliminates the need for auxiliary. See how researchers are using the miseq system and access related product literature, videos, and webinars. View benchtop and productionscale sequencer comparison tables, and find tools designed to help you choose the right platform for your needs. A comparison of absolute sequence lengths for assembled pairedend miseq reads and unidirectional reads from the ion torrent pgm platform derived from a mockcommunity mixture of 20 bacterial dnas. Choosing the right ngs sequencing instrument for your study.
Sales of the ion torrent desktop sequencers exceed those of its rival miseq machine from illumina, according to a new financial report, which highlights encouraging trends for both illumina and ion torrent parent company, life technologies. Comparing apples and oranges next generation sequencing. Pdf comparison of nextgeneration sequencing systems. Comparison of illumina miseq, ion torrent pgm, 454 gs. The miseq is the costeffective alternative that delivers 25 million reads with 300 base pair read length from each end.
The iontorrent sequencing run itself is much shorter hours versus days. They compared the results obtained with those platforms to the performance of the illumina hiseq, the current market leader. More hands on time, and fewer overall bases of data than illumina. Accelerating science behind the bench lab tips and tricks when do i use sanger sequencing vs ngs. Ion torrent pgm vs pacbio vs miseq lost in replications. Four different types of illumina sequencing platforms miseq, nextseq, iseq, novaseq and one ion torrent sequencing instrument s5 were involved in the study. Performance comparison of illumina and ion torrent next. Highthroughput sequencing of the taxonomically informative 16s rrna gene provides a powerful approach for exploring microbial diversity. Accompanying the fastq and bam files is a presentation, the first half of which compares the performance to big brother hiseq. Illumina has released a miseq dataset for li mg1655 on its website.
Im looking to sequence my samples on an illumina platform but i dont know whether to use miseq or hiseq. Here is a publication comparing the performance of different sequencing platforms. Prior studies have compared these two sequencing platforms for various. A comparison of illumina and ion torrent sequencing platforms in. I admit my own bias, and for today suffice it to say that each platform in terms of technology has an accuracy rate on the order of 99%. Ion pgm has accessory equipment that might no longer be needed. The number of reads per sample after filtering varied from 31,049 to 223,587, with 83% illumina and 75% ion torrent of the samples having more than 100,000 total reads see table 2. How would you compare the miseq and the hiseq sequencing. The equipment needed for performing an ampliseq for illumina library prep is the same as the equipment needed for performing an ampliseq library experiment on the ion torrent. What is the difference between ion torrent and illumina sequencing. Kallisto, a new ultra fast rnaseq quantitation method. There is a lot of competition in this market mainly between ion torrent and illumina, which nick refers to as lively. These were applied to six human stool samples using illumina hiseq, miseq and ion pgm shotgun sequencing, as well as amplicon sequencing across two variable 16s rrna gene regions.
We analysed the ability to call variants from each platform and found that we could call slightly more variants from ion torrent data compared to miseq data, but at the expense of a higher false positive rate. Performance comparison of benchtop highthroughput sequencing platforms nature biotech. A tale of three next generation sequencing platforms. Illumina dye sequencing is a technique used to determine the series of base pairs in dna, also known as dna sequencing. Here we compare the results obtained with those platforms to the performance of the illumina hiseq, the current market. Comparing the performance of three nextgen sequencers. This approach marries simple chemistry to proprietary semiconductor technology. There is a rebuttal from iontorrent, the analysis section is not as much a rebuttal they are instead saying that the new kits are a lot better.
The miniseq and miseq instruments offer low to mid sample throughput, affordable. The biggest difference is that we can go down to 10ng of dna on the ion torrent platform and still get good results, even if the quality is lower. Though illumina has largely dominated the rnaseq field, the simultaneous availability of ion torrent has left scientists wondering which platform is most effective for differential gene expression dge analysis. Apr 04, 2012 computational biologist mauricio carneiro, phd, describes a broad institute technology comparison to determine how pacific biosciences, ion torrent, and illumina miseq perform in discovering and. If you are lucky enough to have spent upwards of six figures on your mba, you may be tempted to think that it was a waste of money now that the robots are in the process of devouring just about every job there is. We use the illumina miseq platforms for our hematological malignancies, while we use the thermofisher ion torrent pgm and proton platform for our solid tumors. For more information, see the miseq reagent kit support page.
Jul 30, 2014 16s rrna read lengths in miseq and ion torrent sequence data. General overview life technologies now thermofisher expanded their ngs portfolio with the acquisition of ion torrent and their first system, the ion personal. The latest paper in plos one presents a comparison of miseq and proton pi sequencing to detect chromosome abnormalities in selfaborted foetuses. The ion torrent proton compared to the illumina hiseq 2500. Nextgeneration sequencing is a powerful tool for virological surveillance. Mbas happen to be equipped with some very sophisticated. While illumina and ion torrent sequencing platforms are used extensively. Nextgeneration sequencing ngs technology is becoming a powerful tool in a public health setting for virus surveillance. A compact, allinone platform incorporates cluster generation, pairedend fluidics, sequencing by synthesis chemistry, and data analysis. Sequence generated by ion torrent, miseq and pacific biosciences technologies displays near perfect coverage behaviour on gcrich, neutral and moderately atrich genomes, but a profound bias was observed upon sequencing the extremely atrich genome of plasmodium falciparum on the pgm, resulting in no coverage for approximately 30% of the genome. Ion torrent technology directly translates chemically encoded information a, c, g, t into digital information 0, 1 on a semiconductor chip. Comparison of illumina miseq and the ion torrent pgm and. Which one would you recommend illumina miseq or ion. Ion torrents pgm, pacific biosciences rs and the illumina miseq.
What is the difference between ion torrent and illumina. Gs junior from roche, miseq from illumina and pgm from ion torrent. Additionally, the current generation of illumina instruments can generate sequence reads from both ends of a fragment pairedend reads, while ion torrent cannot. Access a list of nextgeneration sequencing products and services used during the sequencing workflow. Comparison of illumina miseq and the ion torrent pgm and s5. Next generation sequencing an overview open source at. Each sample was sequenced on two hts platforms illumina and ion torrent in two replicates. Jul 16, 2012 the ion torrent proton compared to the. Sandeep has the general idea right the miseq and the hiseq use essentially the same chemistry with the hiseq x diverging a bit more as its currently the only system to use patterned flow cells.
1292 510 837 613 832 1564 1186 1372 334 1349 853 1116 757 928 1100 638 67 192 1284 1589 1296 542 449 593 1606 971 22 394 638 1475 617 159 449 477 159 634 513 290 913 908 457 654