Developer: Brian J. Stucky
Supported platforms: Windows, macOS, and Linux (Python / PyGTK)
Download: https://github.com/stuckyb/seqtrace (latest release: v0.9.1)
Features
View Quality scores
Yes. Phred quality scores are used for filtering and highlighting low-quality base calls.
View raw data
No.
Assembly
Yes. Automatically pairs forward and reverse traces, aligns them using a customized Needleman-Wunsch algorithm, and generates consensus sequences.
Input file formats
.ab1 (ABIF), .scf, and .ztr
Output file formats
FASTA and aligned forward/reverse sequences.
Trimming
Yes. Automated Phred quality score filtering and end trimming, plus primer specification in project files.
Integrated Blast
No.
Open multiple windows
Yes, including simultaneous side-by-side viewing of paired forward and reverse traces.
Edit bases
Yes.
ABI limits (regions outside of clear range region are displayed in gray)
No.
Other functions
- Project management for batch processing large sets of forward/reverse reads
- Variable trace zoom and scaling
- Consistent consensus calling across paired reads
Cost
Free and open source (GPLv3 or later).
Comments
SeqTrace goes beyond basic single-trace viewing by automating forward/reverse read pairing, trimming, and consensus sequence generation. Note that the desktop codebase (last updated in 2018) relies on Python 2 / PyGTK, so setup on modern systems may require a compatible legacy runtime or Windows installer.
Return to the Trace Viewers overview or check trace quality online with QualTrace III Online.