The landscape of chloroplast genome assembly tools

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. The examination of 105 data sets from species with unknown plastid genomes led to the assembly of 20 novel chloroplast genomes. We created docker images for each tested tool that are freely available for the scientific community and ensure reproducibility of the analyses. These containers allow to analyze and screen data sets for chloroplast genomes using standard computational infrastructure. Thus, large scale screening for chloroplasts as hidden treasures within genomic sequencing data is feasible.