bioRxiv preprint doi: https://doi.org/10.1101/665869; this version posted May 20, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Freudenthal et al. RESEARCH The landscape of chloroplast genome assembly tools Jan A Freudenthal1,2, Simon Pfaff1,3, Niklas Terhoeven1,2, Arthur Korte1, Markus J Ankenbrand1,2,4y and Frank F¨orster1,3,5,6*y *Correspondence:
[email protected] Abstract giessen.de 6Bioinformatics Core Facility of Chloroplasts are intracellular organelles that enable plants to conduct the University of Gießen, photosynthesis. They arose through the symbiotic integration of a prokaryotic cell Heinrich-Buff-Ring 58, 35392 into an eukaryotic host cell and still contain their own genomes with distinct Gießen, Germany Full list of author information is genomic information. Plastid genomes accommodate essential genes and are available at the end of the article regularly utilized in biotechnology or phylogenetics. Different assemblers that are yCorresponding author able to asses the plastid genome, have been developed. These assemblers often use data of whole genome sequencing experiments, which usually contain reads from the complete chloroplast genome. The performance of different assembly tools has never been systematically compared. Here we present a benchmark of seven chloroplast assembly tools, capable to succeed in more than 60 % of known real data sets. Our results show significant differences between the tested assemblers in terms of generating whole chloroplast genome sequences and computational requirements.