Developer: GEAR Genomics / EMBL (Tobias Rausch & collaborators)
Supported platforms: Web browser (Windows, macOS, Linux, ChromeOS)
Access: Indigo | Sage | Pearl (complements Teal)
Features
View Quality scores
Yes. Displays base and variant quality metrics across outputs and hover tooltips, and exports VCF quality scores (detailed trace QC is handled cleanly in companion Teal or Tracy).
View raw data
Displays interactive four-channel trace curves and secondary peak decomposition plots rather than unprocessed capillary sensor sweeps.
Assembly
Yes, specialised across three apps: Indigo performs rapid single-trace variant discovery and heterozygous indel allele phasing/deconvolution; Sage aligns single traces to whole pre-indexed genomes, custom FASTA, or wildtype chromatograms; Pearl aligns multiple traces against a reference to inspect coverage and patch mismatches (or compute an assembled consensus).
Input file formats
.ab1, .abi, .ab!, .ab, .scf, plus FASTA references (and pre-indexed genome references inside Indigo/Sage).
Output file formats
Aligned chromatograms, phased allele alignments, patched consensus FASTA (Pearl), and variant calls/tables.
Trimming
Configurable left/right trim parameters (and secondary-peak threshold defaults such as 33% in Indigo) prior to alignment.
Integrated Blast
Uses built-in FM-index whole-genome anchoring rather than external NCBI BLAST.
Open multiple windows
Yes, across browser tabs and multi-trace views in Pearl.
Edit bases
Yes in Pearl, which supports interactively jumping between read/reference conflicts and patching the consensus sequence.
ABI limits (regions outside of clear range region are displayed in gray)
No (uses user-configured trim lengths).
Other functions
- Indigo: Interactive indel-length decomposition curve and dbSNP
rsannotation - Sage: Colour-coded match, mismatch (red), and heterozygous secondary-peak (orange/yellow) trace alignment
- Pearl: Interactive green/red coverage map and conflict-stepper for plasmid/reference verification
Cost
Free and open source; the web applications use GPL-3.0, while current Tracy uses BSD 3-Clause.
Comments
While Teal handles straightforward trace inspection, Indigo, Sage, and Pearl make EMBL’s GEAR Genomics suite one of the strongest free browser ecosystems for real molecular workflows—especially CRISPR/indel phasing (Indigo), genome anchoring (Sage), and multi-read clone verification (Pearl).
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.