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Ion Personal Genome Machine and Proton sequencing data analysis

eagle-i ID

http://eagle-i.itmat.upenn.edu/i/00000138-de73-ae2d-eb5b-b63c80000000

Resource Type

  1. Data analysis service

Properties

  1. Fee for service
    Yes
  2. Resource Description
    "Torrent Suite, the Torrent server analysis pipeline is the primary software used to process raw data acquired by PGM/Proton sequencer to produce read files containing high quality bases. The base calls are in both SFF and FASTQ file formats for easy downstream analysis with third party analysis tools. The Torrent browser provides many matrices, graphs and reporting features derived from the pipeline results. Filtering and trimming: This is done to remove low quality bases or uncertain base calls by filtering out entire reads and trimming low quality 3’ ends of reads respectively. The SFF files contain per-base quality scores along with all other read information. The FASTQ files also provide per-base quality scores. TMAP: Torrent Mapping Alignment Program implements a two-stage mapping approach – reads that do not align during the 1st stage are passed to the 2nd stage with a new set of algorithms and/or parameters. Overall the alignment provides an index to determine run and library quality. Variant Caller: After analysis the variant caller generates a report of the SNVs and the insertion-deletions obtained from the data set (Torrent Suite User Documentation, Life Technologies). Commercial software NextGene, DNASTAR, PARTEK and others are available for analysis of PGM/Proton data. We provide data analysis service for a fee using Torrent suite, NextGene and other software."
  3. Service Fee URL
    http://www.med.upenn.edu/genetics/dnaseq/pricing.shtml
  4. Related Resource
    Ion Personal Genome Machine Sequencer
  5. Related Resource
    Ion Torrent Proton
  6. Service Provided by
    DNA Sequencing Facility (Penn)
  7. Website(s)
    http://www.med.upenn.edu/genetics/dnaseq/Proton.shtml
  8. Website(s)
    http://www.med.upenn.edu/genetics/dnaseq/ion.shtml
  9. Related Technique
    Bioinformatics analysis
  10. Related Technique
    DNA sequencing assay
 
RDFRDF
 
Provenance Metadata About This Resource Record
  1. workflow state
    Published
  2. contributor
    fcoldren
  3. created
    2012-07-31T14:17:57.475-05:00
  4. creator
    fcoldren
  5. modified
    2015-06-08T11:01:06.237-04:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016