Comaprison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC

we compared hybrid assemblies for 6 bacterial isolates, including the reference strains Escherichia coli using next generation sequencing (NGS) short reads sequencing, single tube long fragment reads (stLFR) sequencing and Oxford Nanopore Technologies (ONT) sequencing platforms. We obtained the complete genomes assembled by the hybrid assembler Unicycler using ONT and NGS reads, and the other complete genomes de novo assembled by using stLFR and ONT reads. Meanwhile, the long-read-only assembly genomes by Canu with NGS reads base correction, the chromosome-level assembly genomes by Athena with stLFR reads and the draft assembly genomes by SPAdes with NGS data were obtained for the 3 different sequencing strategies comparison.

本研究针对6株细菌分离株（含参考菌株大肠杆菌（Escherichia coli））开展混合组装对比分析，所用测序平台涵盖下一代测序（Next Generation Sequencing，NGS）短读长测序、单管长片段读长测序（single tube long fragment reads，stLFR）以及牛津纳米孔科技（Oxford Nanopore Technologies，ONT）测序平台。本研究通过混合组装工具Unicycler，利用ONT与NGS读段组装得到完整基因组；同时借助stLFR与ONT读段，经从头组装（de novo）方式获得其余完整基因组。此外，为开展三种不同测序策略的对比分析，本研究还得到三类组装结果：经NGS读段碱基校正后，由仅长读长组装工具Canu组装得到的仅长读长组装基因组；由Athena利用stLFR读段组装得到的染色体水平组装基因组；以及由SPAdes利用NGS数据组装得到的草图组装基因组。