Applied Biosystems™ Analysis Module Variant Analysis (VA) is Sanger sequencing software hosted on the Thermo Fisher Cloud environment. VA can be accessed for free through the Apps Page. 1000 AB sequencing files can be analyzed and results displayed in 1 minute, while 10,000 AB sequencing files can be analyzed in less than 5 minutes, a rate that cannot be matched by traditional desktop software.

Access VA software for free >

Variant Analysis software is designed for reference-based re-sequencing analyses such as SNP detection and analysis, SNP discovery and validation, and sequence confirmation, all on the cloud. The software can automatically retrieve reference sequence from genomic databases, report variants in genomic coordinates, and report genomic annotations for SNPs. The software also generates and can export variants in the standard variant call format (vcf). With highly overlapped forward/reverse strands, Variant Analysis software reports higher sensitivity for SNPs than Variant Reporter.

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

Key software features:
• Simplified workflow that requires less than a half hour to learn
• No operating system limitation (including iOS). Software accessed through a web browser.
• No software maintenance needed from user
• 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
• Increased analysis capacity with the power of the cloud

What’s new in Variant Analysis 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.