Ion Torrent™

NextGENe™ Software for Ion Torrent™ Academic/Network License

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NextGENe® Software for Ion Torrent™ is a free standing, biologist-friendly Windows®-based analysis package for Ion Torrent™ systems. The software is based upon many proprietary technologies for increased accuracy and analysis speed of Ion Torrent™ semiconductor sequencing data. The software requires little or no bioinformatics support and presents results in a highly graphical and interactive user interface.

NextGENe® Software for Ion Torrent™ comes with the following:

Application Modules:
• De novo assembly
• SNP⁄Small and Large InDel Detection of Whole Genome and Amplicon Sequencing
• Exome Assembly and Variant Discovery
• RNA-Seq including Variant Discovery, Splicing Variant Analysis, Novel Exon⁄Gene Discovery, Fusion Transcript Discovery, and Expression Analysis
• Metagenomic Analysis
• miRNA Discovery and Quantification
• ChIP-Seq

Specialized Tools:
• Condensation Tool for local assembly, read elongation, and error correction
• Project Comparison of up to 10 individual sequences
• Scoring of found variants for filtering
• Paired End sequence merge tool
• Highly graphical linked reporting of sequence analysis
• Automated sorting of Bar Code⁄Index Tag
• Modified 3-step Burrows Wheeler Alignment Algorithm
• Family Analysis Tool for personalized medicine and filtering templates of up to 5 individuals for rare diseases
• Unattended analysis of multiple sequence samples, with unattended alignment to separate references
• Importation and comparison of Analyzed Sanger Sequencing Reads of multiple analysis
• Point and Click analysis set up requiring no scripting
• Use of pre-indexed annotated genomes for rapid analysis
• Pre-Indexed reference genomes supplied
• Dual Reference acceptance
• Import⁄export in SAM⁄BAM format

Mutation Report Filters:
• CDS +⁄– n bases
• mRNA +⁄– n bases
• Regions of Interest (ROI in GBK File or BED file)
• Substitutions (Synonymous, Mis-sense, Nonsense)
• Indels
• Homozygous vs. Heterozygous
• Reported vs. Unreported
• Added Automatically
• Added Manually
• Confirmed
• Deleted
• Negative SNPs (Reported variants that are not found)

Mutation Score Filters:
• Coverage Score
• Read Balance Score
• Allele Balance Score
• Homopolymer Score
• Mismatch Score
• Wrong Allele Score

Variant Comparison Report Filters:
• All Mutation Report Filters
• Shared vs. Differences between projects
• Minimum Coverage
• Percentage Change
• Display Low Coverage Variants

Family Comparison Filters:
• Classify templates (for example, x-linked recessive, autosomal dominant, and compound heterozygous)
• Set requirements for each patient (for example, father is heterozygous, son is homozygous)
• When all criteria are satisfied
• When a conflict is found
• When some information is not available (for example, below coverage)
• Minimum Coverage threshold

Hardware Specifications:

• Dual Core Processor
• 64-bit Windows XP, Windows Vista, or Windows 7
• 4-6 GB RAM
• 1 TB Hard Drive

• Dual Core Processor
• 64-bit Windows XP, Windows Vista, or Windows 7 running in Boot Camp, Parallels®, or VMware® Fusion
• 4-6 GB RAM
• 1 TB Hard Drive

For Research Use Only. Not for use in diagnostics procedures.
For Research Use Only. Not for use in diagnostic procedures.


For Use With (Equipment): Ion PGM™ System, Ion Proton™ System
Software Type: Sequencing Data Analysis
License Type: Academic, Network
Operating System: Windows 7, Windows Vista, Windows XP
Product Line: Ion Torrent™, NextGENe®, Personal Genome Machine (PGM™)
Product Size: 1 software
Software Category: Software
Shipping Condition: Room Temperature


Manuals & protocols