Versatile tools for masking and annotation of plastid genomes: cpanno and masker

Versatile tools for masking and annotation of plastid genomes: cpanno and masker. Markus Kiefer*, Christiane Kiefer, Marcus A. Koch Universität Heidelberg, Centre for Organismal Studies (COS), 69120 Heidelberg, Germany * Author for correspondence cpanno.py is a Python helper script to transfer annotation from a reference to (e.g.) an assembled sequence via a Genbank GFF table. Generation of a graphical overview is possible. As prerequisites it relies on the MAFFT alignment program, the Biopython module and the seqret tool from the EMBOSS package. A usage message is implemented to output program options. masker.sh is a BASH shell script that uses seqret from the EMBOSS package, the Python script cpanno and bedtools to mask uncallable regions in an assembly. If indels are present in the de novo assembled sequence relative to the reference sequence used in a reference based assembly, the positions to be masked will be adjusted accordingly. A usage message is implemented to output program options. The tools have been successfully tested and used (cited there as inhouse scripts): cpanno: Stein R.E., Luque-Fernández C.R., Kiefer, C., Möbus J., Pauca-Tanco G.A., Jabbusch S., Harpke D., Bechteler J., Quandt D., Villasante F., Koch M.A. (2023) Climate-driven past and present interspecies gene flow may have contributed to shape microscale adaptation capacity in Tillandsia lomas in hyperarid south American desert systems. Global and Planetary Change, https://doi.org/10.1016/j.gloplacha.2023.104258 cpanno and masker: Hendriks K.P., Kiefer C., Al-Shehbaz I.A., Bailey D., Hooft van Huysduynen A., Nikolov L.A., Nauheimer L., Zuntini A.R., German D.A., Franzke A., Koch M.A., Lysak M.A., Toro-Nunez O., Özudogru B., Invernón V.R., Walden N., Maurin O., Hay N.M., Shushkov P., Mandakova T., Schranz M.E., Thulin M., Windham M.D., Resetnik I., Spaniel S., Ly E., Pires J.C., Harkess A., Neuffer B., Vogt R., Bräuchler C., Rainer H., Janssens S.B., Schmull M., Forrest A., Guggisberg A., Zmarzty S., Lepschi B.J., Scarlett N., Stauffer F.W., Schönberger I., Heenan P., Baker W.J., Forest F., Mummenhoff K., Lens F. (2023) Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Current Biology 33: 1-17. https://doi.org/10.1016/j.cub.2023.08.026 Koch M.A., Kiefer C., Möbus J., Quandt D., Merklinger D., Harpke D., Villasante Benavides F. (2022) Range expansion and contraction of Tillandsia landbeckii lomas in the hyperarid Chilean Atacama Desert indicates ancient introgre