To support multiple input and ouput file formats without requiring the user to install additional software libraries, all file formats were implemented directly in Python as part of the SeqTrace application.
To meet these requirements, SeqTrace follows object-oriented design principles and was implemented in Python ( ) using the cross-platform GTK+ windowing toolkit ( ).
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A secondary goal was to ensure that the SeqTrace source code could be reused easily in other bioinformatics applications. SeqTrace was designed to be a graphical, user-friendly software program that would run on most of the common operating systems in current use. SeqTrace is free and open-source software that runs on all popular operating systems. Although SeqTrace was designed with batch processing in mind, it can also serve as a general-purpose trace viewer and editor. SeqTrace is intended specifically for sequencing projects that require converting trace files directly into high-quality, finished sequences, and it provides a graphical, user-friendly interface for automating the entire process. SeqTrace, a new computer program described in this communication, was created to help fill this gap. Although commercial software is available to handle these tasks, free software options are generally much more limited. If done manually, these steps can be very time consuming, especially for large projects. Paired forward and reverse reads of PCR products are also frequently used to ensure final sequence quality this requires aligning the forward and reverse sequences and determining a single consensus sequence from the pair. At a minimum, this involves inspecting each trace file to identify problematic sequencing runs, remove unreliable base calls, and trim the ends of the sequence. Modern Sanger sequencing instruments, however, generate “raw” chromatogram trace files that require further processing to obtain sequences of sufficient quality for downstream analyses. Many such projects require high-quality sequencing reads from a relatively large number of PCR amplicons. 2 Although high-coverage, high-volume sequencing has largely moved to “next-generation” technologies, Sanger sequencing remains a popular and indispensable tool for low-coverage sequencing applications, such as phylogenetic analyses or DNA barcoding efforts. Since its development in the late 1970s, Sanger chain-termination DNA sequencing 1 has become a widely used, essential technique of molecular biology.
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