ShuffleAnalyzer: A Comprehensive Tool to Visualize DNA Shuffling

DNA shuffling is a powerful technique for generating
synthetic
DNA via recombination of homologous parental sequences. Resulting
chimeras are often incorporated into complex libraries for functionality
screenings that identify novel variants with improved characteristics.
To survey shuffling efficiency, subsequences of chimeras can be computationally
assigned to their corresponding parental counterpart, yielding insight
into frequency of recombination events, diversity of shuffling libraries
and actual composition of final variants. Whereas tools for parental
assignment exist, they do not provide direct visualization of the
results, making the analysis time-consuming and cumbersome. Here we
present ShuffleAnalyzer, a comprehensive, user-friendly, Python-based
analysis tool that directly generates graphical outputs of parental
assignments and is freely available under a BSD-3 license (https://github.com/joerg-swg/ShuffleAnalyzer/releases). Besides DNA shuffling, peptide insertions can be simultaneously
analyzed and visualized, which makes ShuffleAnalyzer a highly valuable
tool for integrated approaches often used in synthetic biology, such
as AAV capsid engineering in gene therapy applications.