SoftGenetics - Software PowerTools for Genetic Analysis






Targeted Resequencing

NextGENe® software includes many useful tools for biologists performing targeted resequencing projects containing single nucleotide polymorphism (SNPs) insertions/ deletions (indels) and large structural DNA rearrangements in sequencing data from Illumina® iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. NextGENe software's Windows® based operation removes the complexity found with programs such as CLC Genomics Workbench, Lasergene's SeqMan Pro, as well as academic software such as MAQ & SOAP, Top Hat, BWA & Bowtie. Biologists simply input the system’s raw reads or BAM files, select the application and click go to begin analysis. Pooled or barcoded samples are quickly de-multiplexed by utilizing the included Barcode Sorting tool, which will separate out each pooled sample for subsequent analysis. NextGENe's Pipeline Tool, AutoRun can be used to set up an unlimited number of consecutive analyses on an unattended basis. Upon completion results are presented in NextGENe software's annotated whole genome browser/viewer for review/editing/commenting.

Specialized resequencing tools include filtering by BED files, Regions of Interest, removal of PCR duplicate reads, and the ability to align to the entire genome or use one or several GenBank (.gb) files.

NextGENe software features greater than 99% accuracy, indel detection up to 33% of read length; rapid review of DNA Variants, nucleotides and Amino Acids; Variant Scoring; Filtering; and analysis comparison. Genome viewer includes links to dbSNP and information from imported tracks, such as COSMIC, dbNSFP, dbSNP, gnomAD and any custom tracks, can be displayed.


For more information Review or Download Application Notes:
Targeted Re-sequencing and Sequence Capture Analysis
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
Reducing error of NGS Sequencing data with NextGENe Condensation™ Tool
NextGENe Illumina SNP_Indel_Detection
Demultiplexing Illumina® MiSeq™ Data
Structural Variant Analysis
Finding Causative Mutation Candidates from NGS Sequencing
NextGENe software Variant Comparison Tool
Mutation Confidence Scoring with NextGENe software
NextGENe SNP & Indel Viewer
Deep Sequence Analysis with NextGENe software
Whole Genome Alignment with NextGENe software
Paired end read merging with NextGENe software
Sequence Analysis Using Barcode/Index Tags of Pooled Samples with NextGENe Software
Using NextGENe software's Pipeline Automation Tool
Analyzing Sequence Data from GS GType Targeted Sequencing of Leukemia-Associated Genes
Processing Ion AmpliSeq™ Data using NextGENe® Software v2.3.0


View live webinars
Target Capture Analysis Part 1 (View) (view on )
Target Capture Analysis Part 2 (View) (view on )
Target Capture Analysis Part 3 (View) (view on )
Processing HaloPlex™ Target Enrichment Panel Data (View) (view on )
Analyzing Ion Torrent AmpliSeq Data (View) (view on )

Creating Sequence Alignment Projects with NextGENe (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




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SoftGenetics - Software PowerTools for Genetic Analysis

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Phone: 814-237-9340 or 888-791-1270


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