Developer: QIAGEN Digital Insights
Supported platforms: Windows, macOS, and Linux
Features
View Quality scores
Yes. Imports quality values from trace files, retains them even in trace-stripped high-throughput imports, and uses quality scores for end trimming and conflict resolution.
View raw data
Standard import retains four-colour chromatograms over the called base span (note that pre-trimmed uncalled trace ends are omitted, and the High-Throughput Sanger importer strips traces to conserve memory).
Assembly
Yes. Supports both de novo Sanger contig assembly (Assemble Sequences) and reference mapping (Assemble Sequences to Reference), plus full NGS/long-read workflows.
Input file formats
.ab1, .abi, .ab, .scf (SCF 2.0/3.0), Phred (.phd), .gz archives, FASTA, FASTQ, GenBank, EMBL, and raw text sequences.
Output file formats
SCF 3.0 (.scf with chromatograms), FASTA (optionally excluding trimmed ends), FASTQ, GenBank, EMBL, CLC (.clc), and CSV.
Trimming
Yes. Quality, ambiguity, and VecScreen-style vector trimming using non-destructive trim annotations.
Integrated Blast
Yes. Runs both remote NCBI BLAST and local blast+ searches against custom or downloaded databases directly inside the workbench.
Open multiple windows
Yes, across synchronised Navigation Area, contig alignment, trace, and BLAST result views.
Edit bases
Yes, directly inside aligned sequences and contigs alongside the trace view.
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 non-destructive trim annotations.
Other functions
- Reusable workflow templates such as Trim and Map Sanger Sequences
- Extensive NGS, RNA-seq, variant calling, and primer design tools in the same environment
- Direct SCF 3.0 trace export
Cost
Paid analysis software with a 14-day free trial (custom quote-based licensing). A free Viewing Mode supports viewing supported data types, export, selected imports, and basic tools; full analysis requires a licence.
Comments
QIAGEN CLC Genomics Workbench is an enterprise bioinformatics platform built primarily for NGS pipelines, yet its Sanger module remains comprehensive—even exporting SCF3 chromatograms and supporting local BLAST databases. For labs strictly doing Sanger sequencing, lighter tools such as ChromasPro, CodonCode Aligner, or UGENE are far more cost-effective.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.