SoftGenetics - Software PowerTools for Genetic Analysis


SNP & INDEL discovery with Ion Torrent PGM & Proton data

Ion Torrent systems are fundamentally different from most other sequencing systems. It is a "post-light" technology because it doesn't depend on detection of light emission from nucleotide incorporation. Instead, it uses a silicon chip containing millions of individual pH meters. Its flow-based approach detects pH changes caused by release of hydrogen ion during incorporation of unmodified nucleotides in DNA replication. Because of this different approach to sequencing, the instrument and reagents are much less expensive and it has a unique error profile- most errors are indels rather than substitutions, especially in homopolymer regions. SoftGenetics has created Ion Torrent specific algorithms to best handle the Ion Torrent data profile, improving the data quality to greater than 99.8%, when paired end reads are used.


NextGENe will quickly de-multiplex pooled or barcoded samples for individual analysis. The included Pipeline Tool can be employed to create multiple sequential analysis projects.


For further information please review or download the following Application Notes:
NextGENe Software AmpliSeq CNV detection Application Note
Assembly of Ion PGM reads with the Floton assembler

de Novo Small Genome Assembly using the Foton™ Assembler in NextGENe® Software
Alignment of PGM PE reads with NextGENe software
Processing Paired End Sequencing Data from the Ion PGM™ Sequencer with NextGENe® Software
Processing Ion PGM™ Sequencing Data with NextGENe Software
Processing CFTR Amplicon Data from the Ion PGM™ using NextGENe® Software
Processing Ion AmpliSeq™ Cancer Panel Data using NextGENe® Software
Amplicon Sequence Analysis of Sanger Sequences and Ion PGM data
Finding Causative Mutation Candidates from NGS Sequencing
NextGENe software Variant Comparison Tool
Mutation Confidence Scoring with NextGENe software
NextGENe SNP & Indel Viewer
Sequence Analysis Using Barcode/Index Tags of Pooled Samples with NextGENe Software
Variant Filtering with NextGENe software
Using NextGENe software's Pipeline Automation Tool
Plugin for Torrent Browser automation
Processing Ion AmpliSeq™ Data using NextGENe® Software v2.3.0


Read Articles:

View Analysis Webinars on processing Ion Torrent data:

  • Ion Torrent data processing (View)
  • CNV Detection using Ion AmpliSeq™ panels or the HaloPlex™ Target Enrichment System Targeted Sequencing Data with NextGENe® Software (View) (view on )
  • Analyzing Ion Torrent AmpliSeq Data with NextGENe Software (View) (view on )

Pricing & Trial Version:
Request 30-day trial/Price Quote


Reference Material:
Download/View NextGENe® Brochure
NextGENe User Manual
Annotated Reference Genomes


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SoftGenetics - Software PowerTools for Genetic Analysis




SoftGenetics - Software PowerTools for Genetic Analysis





SoftGenetics - Software PowerTools for Genetic Analysis

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