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Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome
3 Biotech ( IF 2.8 ) Pub Date : 2020-10-19 , DOI: 10.1007/s13205-020-02474-0
Seung Chul Shin 1 , Woong Choi 2 , Junhyuck Lee 2, 3 , Hyo Jin Kim 4, 5 , Han-Woo Kim 2, 3
Affiliation  

We sequenced the Paenibacillus sp. R4 using Oxford Nanopore Technology (ONT), single molecule real-time (SMRT) technology from Pacific Biosciences (PacBio), and Illumina technologies to investigate the application of nanopore reads in de novo sequencing of bacterial genomes. We compared the differences in both genome sequences between genome assemblies using nanopore and PacBio reads and focused on the difference in the prediction of coding sequences. The results indicated that for more accurate predictions of open reading frames, contigs in the assemblies using only PacBio reads also needed to be corrected using short reads with high-quality bases, and repeat regions in genomes did not affect the increase of mispredicted coding sequences via genome polishing significantly. In assemblies using only nanopore reads, genome polishing was essential, but many repeat regions in genomes might increase the number of mispredicted coding sequences via genome polishing. The hybrid assembly combining the long reads and short reads represents the best result for coding sequence predictions in genome assemblies using nanopore reads.



中文翻译:

评估结合长读长和短读长获得类芽孢杆菌的组装方法。R4高质量全基因组

我们对类芽孢杆菌进行了测序sp. R4 使用牛津纳米孔技术 (ONT)、Pacific Biosciences (PacBio) 的单分子实时 (SMRT) 技术和 Illumina 技术研究纳米孔读数在细菌基因组从头测序中的应用。我们使用纳米孔和 PacBio 读数比较了基因组组装之间两个基因组序列的差异,并重点关注编码序列预测的差异。结果表明,为了更准确地预测开放阅读框,仅使用 PacBio 读取的程序集中的重叠群也需要使用高质量碱基的短读取进行校正,并且基因组中的重复区域不会影响错误预测编码序列的增加。基因组抛光显着。在仅使用纳米孔读数的组装中,基因组抛光是必不可少的,但是基因组中的许多重复区域可能会通过基因组抛光增加错误预测的编码序列的数量。结合长读取和短读取的混合组装代表了使用纳米孔读取进行基因组组装中编码序列预测的最佳结果。

更新日期:2020-10-19
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