The threshold value represents the sensitivity of the sequencing error detection mechanism. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. Initially, the program scans a given multiple sequence alignment (MSA) for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. To provide users full control over the error correction process, a fully automated error correction algorithm has not been implemented. Here, we introduce ChromatoGate (CG), an open-source software that accelerates and partially automates the inspection of chromatograms and the detection of sequencing errors for bidirectional sequencing runs. As sequence numbers and lengths increase, visual inspection and manual correction of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is required. They also generate data that translates the chromatograms into molecular sequences of A, C, G, T, or N (undetermined) characters. Automated DNA sequencers generate chromatograms that contain raw sequencing data.
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