Developer: Thermo Fisher Scientific (Applied Biosystems)
Supported platforms: Web browser (Windows, macOS, Linux, ChromeOS); optional Windows Connect Transfer uploader
Access: https://www.thermofisher.com/us/en/home/digital-science/thermo-fisher-connect.html
Features
View Quality scores
Yes. The Quality Check (QC) app summarises trace quality across plates, flags borderline/failed reads against configurable thresholds, and displays per-base quality scores alongside electropherograms.
View raw data
Yes. The Quality Check app’s single-trace details include Analyzed, Raw, and Analyzed+Raw views. When comparing multiple traces, only analysed data is displayed.
Assembly
Yes, for reference alignment workflows—the Variant Analysis (VA) app aligns forward and reverse .ab1 reads against retrieved genomic references to call SNPs and indels (while Next-Generation Confirmation verifies NGS VCF calls).
Input file formats
.ab1 (plus .fsa in companion Fragment Analysis / Peak Scanner apps and .vcf for NGS confirmation).
Output file formats
.vcf variant calls, QC summary reports, and cloud project exports.
Trimming
Yes—threshold-based quality flagging and read exclusion/trimming inside Quality Check and Variant Analysis.
Integrated Blast
Automatic genomic reference retrieval in Variant Analysis rather than open-ended NCBI BLAST.
Open multiple windows
Yes, across browser tabs and multi-trace study panels.
Edit bases
Yes, inside the QC and Variant Analysis review panes.
ABI limits (regions outside of clear range region are displayed in gray)
Import and display of instrument ABI clear-range tags is not confirmed; the application provides its own KB/QC trim and flag thresholds.
Other functions
- Cloud storage and plate-level Trace QC sharing directly from Applied Biosystems genetic analysers
- Automated SNP/indel annotation and bidirectional concordance confirmation
- Also complemented in Thermo Fisher’s ecosystem by the newer browser-based InnoviGene Suite
Cost
Free Individual account (requires registration; current Individual accounts include 25 GB of free cloud storage, while older core facility documentation previously cited 1 TB). Paid storage upgrades and Team/Enterprise subscriptions are available.
Comments
Thermo Fisher Connect effectively fills the modern browser gap left by the discontinued desktop Seq Scanner. It is ideal for core facilities and Applied Biosystems sequencer users who want cloud plate-QC summaries and Variant Analysis without Windows-only desktop installers.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.