SeqTrace is an application for viewing and processing DNA sequencing chromatograms (trace files). SeqTrace makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA.
SeqTrace also includes a full-featured trace file viewer and editor. You can view your sequencing chromatograms at a variety of scales and zoom levels, simultaneously view matching forward and reverse traces, edit the called bases, and export individual DNA sequences as well as forward/reverse alignments. SeqTrace supports popular trace file formats, including ABIF, SCF, and ZTR.
To get started using SeqTrace, see the quick start guide, read the installation instructions, or browse the full user documentation.
Click the image above to see a full scale screen shot of SeqTrace running on XUbuntu 11.10. You can also see screen shots of SeqTrace running on other operating systems.
SeqTrace is written in Python, uses PyGTK with the GTK+ windowing toolkit, and runs on most popular operating systems, including GNU/Linux, Windows, and OSX. I welcome feedback, bug reports, or code contributions from users. To submit bug reports, please use SeqTrace's issue tracking system. To get in touch with me directly, see the project information page to read more about SeqTrace and how to contact me.
SeqTrace 0.9.1 is now available for download. This new release does not introduce any major new features, but it does include several important improvements and bug fixes. For many users, the most notable improvements are likely to be the various ways in which support for SCF input files has been enhanced. SeqTrace 0.9.1 also fixes a critical bug that caused some of the settings controls to display incorrectly under recent versions of the GTK+ toolkit on Linux. For full details of the improvements in 0.9.1, see the release history. This will be the last release of SeqTrace to use the GTK+ 2 toolkit and PyGTK.
It's been almost two years since the last release of SeqTrace, and after a lot of work, I'm very pleased to announce that SeqTrace 0.9.0 is now available. This is a significant upgrade that includes many important improvements and new features as well as a few relatively minor bug fixes. I'd like to express my appreciation to all of the users who took the time to give me feedback on SeqTrace 0.8; your ideas and comments were very helpful in deciding what to focus on for 0.9.0. You can read about all of the new features in SeqTrace 0.9.0 in the release history.
SeqTrace 0.8.1 fixes several bugs present in the 0.8.0 release. For full details, see the release history.