Developer: Tobias Rausch / GEAR Genomics (EMBL)
Supported platforms: Linux, macOS, and Windows (command-line binary / Bioconda / Docker / C++ source)
Download: https://github.com/gear-genomics/tracy
Features
View Quality scores
CLI engine—reads and outputs per-base Phred quality values inside FASTQ, JSON, and VCF/BCF outputs (visual browsing of Tracy’s output is handled by the companion web viewers Teal and Indigo/Sage/Pearl).
View raw data
Exports processed A/C/G/T trace intensities (DATA.9–12 channels), base-call positions, and peak heights programmatically into structured JSON or TSV files.
Assembly
Yes—supports trace basecalling (tracy basecall), reference alignment against indexed genomes or FASTA (tracy align), heterozygous indel deconvolution (tracy decompose), and multi-trace assembly (tracy assemble).
Input file formats
.ab1, .abi, .ab!, .ab, and .scf.
Output file formats
JSON, TSV, FASTA, FASTQ, aligned consensus FASTA, and BCF/VCF variant calls.
Trimming
Configurable left/right trim parameters and quality-trimmed core alignment anchoring via CLI flags.
Integrated Blast
Uses local FM-index whole-genome matching rather than remote NCBI BLAST.
Open multiple windows
Command-line tool (no native GUI window).
Edit bases
Automated basecalling and secondary-peak calling (re-calls primary/secondary sequences by peak ratio threshold) rather than manual GUI editing.
ABI limits (regions outside of clear range region are displayed in gray)
No.
Other functions
- Powers the entire EMBL GEAR Genomics web suite (Teal, Indigo, Sage, and Pearl)
- Scriptable batch processing of large chromatogram directories in bioinformatics pipelines
- Available via Conda (
bioconda::tracy) and container images
Cost
Free and open source (BSD 3-Clause).
Comments
Tracy is not a graphical trace viewer itself, but it is the open-source command-line engine behind EMBL’s GEAR Genomics web tools. Bioinformaticians who want to extract processed trace intensities to JSON/TSV, batch-align traces against whole genomes, or automate Sanger indel variant calling (VCF) in Nextflow/Snakemake pipelines will find Tracy well suited to scripted workflows.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.