The Ion Proton™ Sequencer

Published: October 15th, 2014

Category: All News, Announcements, Featured News, NextGen DNA Sequencing

The ICBR Nextgen DNA Sequencing core offers University of Florida researchers and core customers the most up-to-date platforms. With this commitment, ICBR now provides additional high-throughput sequencing with the Life Technologies Thermo Fisher Ion Proton™. The instrument is based on the same semiconductor technology as the Ion PGM™ System, but can perform much higher throughput sequencing runs.

The Ion Proton™ I Chip (available now) can generate 60-80 million passing filter reads and is ideal for sequencing both exomes – regions in the DNA that code for proteins – and small genomes. The Ion Proton™ II Chip is expected to become available in the near future and will be ideal for sequencing whole human genomes. Additionally, the Ion Proton™ OneTouch™ system automates most of the template prep process, while the stand-alone Ion Proton™ Torrent Server performs primary and secondary data analysis.

The Ion Proton™ sequencer works in conjunction with the Ion Reporter analysis software, which is free for users, to conveniently analyze data for many sequencing applications. This stand-alone server eliminates the informatics bottleneck, high capital and IT investment associated with optical-based sequencers. Sequencing speed is reduced dramatically (2-4 hours per run) with the introduction of next-generation Ion Torrent™ semiconductor chip technology, in which no lasers or fluorescently labeled nucleotides are necessary.

Ion Proton™ System performance specifications with Ion PI™ Chip
Throughput Up to 10 Gb (Ion PI™ Chip)
The Ion PII™ Chip* will enable sample-to-variant analysis of a human genome in a single day, at up to 20x coverage.
Read length Up to 200-base fragment reads
Number of reads passing filter (PI chip) 60-80 million reads passing filter
Sequencing run time 2-4 hours
Key applications Human-scale genome sequencing ChIP sequencing
Whole transcriptome sequencingExome sequencing
Methylation analysisGene expression by sequencing
Small genome sequencingDe novo sequencing
Small RNA sequencingGene sequencing
Areas of interest Agricultural research Stem cell research
Cancer research Epigenomics Ancient DNA genomics
Forensic scienceMetagenomics
Barcoding solutions 384 barcodes supported by Torrent Suite Software
96 off-the-shelf barcodes for DNA
16 off-the-shelf barcodes for RNA
Software solutions Torrent Suite Software utilizing Torrent Browser including TMAP alignment and Torrent Variant Caller for germline or somatic mutation detection.Torrent Browser (included) offers users remote web access to instrument status monitoring, run quality reports, individual data files, and extensible plug-ins for application-specific analysis.Plugins available for download from the Torrent Browser Plugin Store for analysis of genome sequencing, targeted sequencing, variant analysis and annotation, microbial sequencing, transfer to 3rd party bioinformatics packages, and more.Data can optionally flow into Ion Reporter™ Software for controlled analysis, annotation, and reporting of variants. Ion Reporter™ Software provides application specific workflows to support single, trio and paired tumor normal analysis
Data formats Industry standard FASTQ, SFF, BAM and VCF format outputs


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