A2G2: A Python wrapper to perform very large alignments in semi-conserved regions

Summary Amplicons to Global Gene ( A 2 G 2 ) is a Python wrapper that uses MAFFT and an “Amplicon to Gene” strategy to align very large numbers of sequences while improving alignment accuracy. It is specially developed to deal with conserved genes, where traditional aligners introduce a significant amount of gaps. A 2 G 2 leverages the add sequences option of MAFFT to align the sequences to a global reference gene and a local reference region. Both of these references can be consensus sequences of trusted sources. Efficient parallelization of these tasks allows A 2 G 2 to align a very large number of sequences (> 500K) in a reasonable amount of time. A 2 G 2 can be imported in Python for easier integration with other software, or can be run via command line. Availability A 2 G 2 is implemented in Python 3 (3.6) and depends on MAFFT availability. Other package requirements can be found in the requirements.txt file at https://github.com/jshleap/A2G . A 2 G 2 is also available via PyPi ( https://pypi.org/project/A2G ). It is licensed under the LGPLv3. Supplementary information Supplementary material is available at github as jupyter notebook.