Analysis Module Next-Generation Confirmation (NGC) Software

Description

Applied Biosystems® Analysis Module Next-Generation Confirmation (NGC) is CE Sanger sequencing software hosted on the Thermo Fisher Cloud environment. NGC can be accessed for free through the Apps Page. It confirms variants generated by:

• Detecting variants from CE sequence ab1 files
• Comparing NGS variants and CE variants
• Generating Venn diagrams for visual confirmation

Access NGC software for free >

With Next-Generation Confirmation software, you can examine variants from a CE electropherogram to confirm the variants detected by NGS platforms. The software takes CE sequencer-generated ab1 files and performs SNP detection and analysis, SNP discovery and validation, and sequence confirmation, all on the cloud. NGC software can automatically retrieve reference sequence from genomic databases, report variants in genomic coordinates, and report genomic annotations for SNPs. The software takes NGS variant vcf files and compares NGS variants and Sanger variants in the same alignment view and can also generate a Venn diagram, allowing the user to visually compare and confirm variants generated from NGS. In addition, the NGC software generates and can export variants in standard variant call format (vcf).

Note: Confirmation of heterozygous deletions and insertions will be supported in future software release.

Key software features:
• Variants generated from NGS platforms confirmed
• Variants generated from NGS and CE platforms displayed in the same view
• Simplified workflow requires less than a half hour to learn
• No operating system limitation (including iOS). Software accessed through web browser.
• No software maintenance needed from user
• Increased analysis capacity through power of the cloud
• Projects can be shared among registered users for collaboration
• Genomic coordinates reported for each variant and genomic annotations automatically retrieved
• Easy navigation to regions of interest in electropherograms
• Simple quality checking by color-coded trace summary and quick look-ups of markers (low QV, user-edited bases, mixed bases, etc.)
• Automatic alignment of multiple analyzed plots, forward or reverse complementary
• Variants exported in standard vcf format

What’s new in Next-Generation Confirmation Module v2.0?
KB Basecaller v1.4.2.2: Basecall your unanalyzed .ab1 traces with reliable QV values or reanalyze with your own basecalling parameters.
Project template selection: Re-use your analysis settings from previous analyzed projects.
Optimized default QC flag settings: Display overall trace quality status with optimized default QC flag settings to support all types of .ab1 files generated from different CE instruments.
Export .ab1 files: Export files in .ab1 format that you can share or re-use for future analyses.
GRCh38 human reference support: Analyze human data using this reference genome to support Primer Designer assays (www.thermofisher.com/primerdesigner). Please see hg38 FAQs for more information.
Import existing project settings: Reuse existing project settings from previous analyses without recreating your preferred analysis settings.
GeneBank file support: Upload GeneBank file to use customized annotations for human and other species.
HGVS support: Report genotypes and amino acid changes in HGVS nomenclature.
Customizable variant reporting: Customize the variants table columns as needed for your tables and reports.
Specimen-level genotype reports: Export genotypes at the specimen level.
Improved reporting for amino acid changes: Report amino acid changes based on mRNA transcript information.
Improved user experience for Ion Reporter™ Software or NGS customers: Directly upload NGS variant file .vcf from Thermo Fisher Cloud if you have already analyzed your NGS data in the cloud.

Specifications

For Use With (Equipment):	310 Genetic Analyzer, 3100 Genetic Analyzer, 3100-Avant Genetic Analyzer, 3700 Genetic Analyzer, 3730 DNA Analyzer, 3500 Genetic Analyzer, 3130 Genetic Analyzer, 3130xl Genetic Analyzer, 3730xl DNA Analyzer
Software Type:	Web Based Software
Type:	Next‐Generation Confirmation (NGC) Module