Background Chloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their own genomes with distinct genomic information. Plastid genomes accommodate essential genes and are regularly utilized in biotechnology or phylogenetics. Different assemblers that are able to assess 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. Results The performance of different assembly tools has never been systematically compared. Here, we present a benchmark of seven chloroplast assembly tools, capable of succeeding 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 leads to the assembly of 20 novel chloroplast genomes. Conclusions We create docker images for each tested tool that are freely available for the scientific community and ensure reproducibility of the analyses. These containers allow the analysis and screening of data sets for chloroplast genomes using standard computational infrastructure. Thus, large scale screening for chloroplasts within genomic sequencing data is feasible.

中文翻译：

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叶绿体基因组组装工具的系统比较

背景叶绿体是使植物能够进行光合作用的细胞内细胞器。它们是通过原核细胞共生整合到真核宿主细胞中而产生的，并且仍然包含具有独特基因组信息的自己的基因组。质体基因组容纳必需基因，并经常用于生物技术或系统发育学。已经开发出能够评估质体基因组的不同组装程序。这些组装程序通常使用全基因组测序实验的数据，其中通常包含完整叶绿体基因组的读数。结果 不同装配工具的性能从未被系统地比较过。在这里，我们提出了七种叶绿体组装工具的基准，能够在超过 60% 的已知真实数据集中取得成功。我们的结果表明，所测试的组装程序在生成整个叶绿体基因组序列和计算要求方面存在显着差异。对来自具有未知质体基因组的物种的 105 个数据集的检查导致组装了 20 个新的叶绿体基因组。结论 我们为每个测试工具创建了 docker 镜像，可供科学界免费使用，并确保分析的可重复性。这些容器允许使用标准计算基础设施分析和筛选叶绿体基因组的数据集。因此，在基因组测序数据中大规模筛选叶绿体是可行的。