Champuru 2: Improved scoring of alignments and a user-friendly graphical interface

TL;DR

Champuru 2 is an improved web tool with a user-friendly interface and advanced algorithms for analyzing mixed DNA sequencing chromatograms, enhancing alignment detection accuracy and usability.

Contribution

It introduces a new version of Champuru with a better GUI and more sophisticated alignment scoring algorithms, supporting analysis of multiple offset pairs.

Findings

Enhanced alignment detection accuracy

User-friendly graphical interface

Supports analysis of multiple offset pairs

Abstract

Champuru is a web software tool that helps determine the two sequences present in mixed Sanger chromatograms obtained by sequencing simultaneously two DNA templates of unequal lengths. A previous version (Champuru 1.0) was published as a simple Perl CGI (Common Gateway Interface) application, but the server hosting it was discontinued, which prompted us to update it and develop it further. The new Champuru 2, implemented in Haxe and hosted at GitHub Pages, offers an improved graphical user interface as well as more sophisticated algorithms to compute alignment scores, making it more efficient at detecting the most likely alignment positions between forward and reverse traces. Champuru 2 now make it possible to analyze other offset pairs than the one detected as most likely by the selected algorithm. Champuru 2 is freely accessible at https://eeg-ebe.github.io/Champuru/, including both a graphical user interface (running a JavaScript version transpiled from the Haxe source code) and a compiled command-line version (obtained by transpiling the Haxe source code into C++).