SoftGenetics - Software PowerTools for Genetic Analysis








Application Notes

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Thank you for visiting! We are always updating our application notes in an effort to supply the latest versions for download, and encourage users to check back frequently to ensure they have the most recent information.


Mutation Surveyor®

  • DNA Mutation and Methylation Quantification Application Note (PDF)
  • Heterozygous DNA INDEL Application Note (PDF)
  • NGRL Technology Assessment (PDF)
  • Sequence Assembly Application Note (PDF)
  • Somatic Mutation Detection Technical Note (PDF)
  • UPMC Validation Poster (PDF)
  • Genetic Diversity Application Note (PDF)
  • Hypervariable Mutation Detection (PDF)
  • Methylation Detection Application Note (PDF)
  • Mitochondrial DNA Sequence Analysis using Mutation Surveyor® Software (PDF)
  • Variant Knowledge Base with External Annotation (PDF)
  • User Management with Audit Trail (PDF)


  • Analysis of Advanta Solid Tumor Assay Samples (PDF)

  • Analysis of Advanta RNA Fusions Assay Samples (PDF)

  • Condensation Application Note (PDF)
  • Format Conversion Application Note (PDF)
  • Illumina SNP & INDEL Detection with NextGENe software (PDF)
  • SNP & INDEL Detection of SOLiD™ System Sequence Data with NextGENe (PDF)
  • SNP & Indel Detection of 454 Sequence Data with NextGENe (PDF)
  • Working with Mutation Scores in NextGENe software (PDF)
  • Working with Capture Data Application Note (PDF)
  • Working with Variant Comparison Tool Application Note (PDF)
  • Structural Variant Detection Application Note (PDF)
  • Merging Paired End Reads Application Note (PDF)
  • De novo Assembly Application Note (PDF
  • De novo Assembly of SOLiD Sequence Reads Application Note (PDF
  • Paired Read Assembly Application Note (PDF)
  • De Bruijn Assembly Application Note (PDF)
  • Whole Genome Application Note (PDF)
  • Transcriptome Analysis Application Note (PDF) 
  • RNA-Seq Analysis with NextGENe Software (PDF)
  • ChIP-Seq Analysis Application Note (PDF)
  • Processing IonTorrent Sequencing Data Application Note (PDF)
  • Amplicon Sequence Analysis of ION PGM data with NextGENe Application Note (PDF)
  • 16S Bacterial Identification Application Note (PDF)
  • Serial Analysis of Gene Expression (SAGE) Application Note (PDF)
  • Small RNA Application Note (PDF)
  • Bar-Coding Application Note (PDF)
  • Deep Sequencing Application Note (PDF)
  • Target Sequencing Analysis Application Note (PDF)
  • Alignment of Paired Read Application Note (PDF)
  • Human Identity Analysis Application Note (PDF)
  • Using NextGENe software's Pipeline Automation Tool (PDF)
  • Demultiplexing Illumina® MiSeq™ Data (PDF)
  • IonPGM PE Alignment (PDF)
  • Ion AmpliSeq  (PDF)
  • Ion CFTR Analysis (PDF)
  • Analyzing Sequence Data from GS GType Targeted Sequencing of Leukemia-Associated Genes using NextGENe® Software (PDF)
  • Finding Causative Mutation Candidates in Rare Disease Studies using NextGENe's Variant Comparison Tool (PDF)
  • NextGENe CNV Detection- Dispersion and HMM (PDF)
  • NextGENe Batch CNV - MLPA Replacement (PDF)
  • HLA Analysis with NextGENe® Software (PDF)
  • Working with Circular Reference Sequences in NextGENe® Software (PDF)
  • Somatic Mutation Analysis from Whole Exome Sequencing Data with NextGENe® Software (PDF)
  • Mutation Detection and CNV Analysis for Illumina Sequencing data from HaloPlex Target Enrichment Panels using NextGENe Software for Clinical Research (PDF)
  • NextGENe® Software Analysis of Solid Tumors and Hematological Cancers Using RainDance ThunderBolts™ NGS Panels (PDF)
  • NextGENe® Software Analysis Using the NEBNext Direct® Cancer Hotspot Panel (PDF)
  • Highly Sensitive Somatic Mutation Detection from Biopsy Samples with Deep Sequencing using NextGENe® Software (PDF)
  • Sensitive Aneuploidy Detection (SAD™) Tool (PDF)
  • Integrating NextGENe® Software with Pathway Studio for Differential Gene Expression and Biological Pathway Analysis (PDF)


  • Fragile X Application Note (PDF)
  • AneuploidyAnalysis GeneMarker software AppNote (PDF)
  • Capillary Tilling Application Note (PDF)
  • DatabaseSearching KinshipAnalysis App Note (PDF)
  • Genotype Merge Tool App Note (PDF)
  • GM Kinship Analysis Application Note (PDF)
  • Haplotype Analysis App Note (PDF)
  • MS-MLPA Application Note (PDF)
  • MLPA Application note (PDF)
  • New Technology Size Calling App Note (PDF)
  • LOH application note (PDF)
  • Microsatellite and Pedigree Technical Note (PDF)
  • AFLP® Application Note (PDF)
  • Yale AFLP Analysis comparison (PDF)
  • MLPA Luminex Application Note (PDF)
  • MSI Application Note (PDF)
  • SBE-SNaPshot™ Application Note (PDF)
  • SNPlex™ Application Note (PDF)
  • SNPWave® Application Note (PDF)
  • T-RFLP Application Note (PDF)
  • Trisomy Application Note (PDF)
  • Clustering Algorithms Application Note (PDF)
  • Analysis of MegaBACE™ Data with GeneMarker® Software Application Note (PDF)


  • Cell Line Authentication (PDF)
  • MixtureAnalysis with GeneMarkerHID (PDF)
  • Crime Scene Suspect Application Note (PDF)
  • Paternity Testing Application Note (PDF)
  • Missing Persons Identification Application Note (PDF)
  • Locus Specific Bracket (LSB) Application Note (PDF)
    Automated Contamination Check Tool in GeneMarker®HID Software (PDF)


  • Tracking Copy Number Variant Data with Geneticist Assistant® NGS Workbench (PDF)
  • Utilizing External Databases in Geneticist Assistant® NGS Workbench (PDF)


  • Structural Variation Detection from Pacific Biosciences Data Using NextGENe®LR Software (PDF)
  • Mitochondrial Mixture Analysis with PacificBiosciences Data Using NextGENe®LR Software (PDF)
  • STR Expansion Analysis of Pacific Biosciences Data Using NextGENe®LR Software (PDF)

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