Champuru 2: Improved Scoring of Alignments and a User-Friendly Graphical Interface.

Abstract

Champuru is a web-based software tool that helps determine the two sequences present in mixed Sanger chromatograms obtained by simultaneously sequencing 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 decommissioned, which prompted us to update Champuru 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. It also compares the distribution of alignment scores to the theoretical expectation for the comparison of two random sequences and uses this comparison to calculate p-values for the offset pairs it detects. Moreover, Champuru 2 now makes it possible to analyse 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++).