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 dbNSFP, dbSNP, gnomAD and any custom tracks, can be displayed.

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

Webinars

• Target Capture Analysis Part 1
• Target Capture Analysis Part 2
• Target Capture Analysis Part 3
• Processing HaloPlex™ Target Enrichment Panel Data
• Analyzing Ion Torrent AmpliSeq Data
• Creating Sequence Alignment Projects with NextGENe

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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