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Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome

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Title
Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome
Other Titles
북극 토양에서 분리한 미생물의 향상된 유전체 지도 작성 방법
Authors
Shin, Seung Chul
Choi, Woong
Lee, Jun Hyuck
Kim, Hyo Jin
Kim, Han-Woo
Subject
Biotechnology & Applied Microbiology
Keywords
Hybrid assembly; Long-read sequencing; Oxford Nanopore technology; Paenibacillus sp.
Issue Date
2020-10
Citation
Shin, Seung Chul, et al. 2020. "Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome". 3 BIOTECH, 10(11): 0-1.
Abstract
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 highquality 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.
URI
https://repository.kopri.re.kr/handle/201206/11851
DOI
http://dx.doi.org/10.1007/s13205-020-02474-0
Appears in Collections  
2020-2020, Application study on the Arctic cold-active enzyme degrading organic carbon compounds (20-20) / Kim, Han-Woo (PN20082)
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