title: Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing.
abstract: BACKGROUND
  Whole genome sequence construction is becoming increasingly feasible because of advances in next generation sequencing (NGS), including increasing throughput and read length. By simply overlapping paired-end reads, we can obtain longer reads with higher accuracy, which can facilitate the assembly process. However, the influences of different library sizes and assembly methods on paired-end sequencing-based de novo assembly remain poorly understood.
  
  
  RESULTS
  We used 250 bp Illumina Miseq paired-end reads of different library sizes generated from genomic DNA from Escherichia coli DH1 and Streptococcus parasanguinis FW213 to compare the assembly results of different library sizes and assembly approaches. Our data indicate that overlapping paired-end reads can increase read accuracy but sometimes cause insertion or deletions. Regarding genome assembly, merged reads only outcompete original paired-end reads when coverage depth is low, and larger libraries tend to yield better assembly results. These results imply that distance information is the most critical factor during assembly. Our results also indicate that when depth is sufficiently high, assembly from subsets can sometimes produce better results.
  
  
  CONCLUSIONS
  In summary, this study provides systematic evaluations of de novo assembly from paired end sequencing data. Among the assembly strategies, we find that overlapping paired-end reads is not always beneficial for bacteria genome assembly and should be avoided or used with caution especially for genomes containing high fraction of repetitive sequences. Because increasing numbers of projects aim at bacteria genome sequencing, our study provides valuable suggestions for the field of genomic sequence construction.
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. afra@mail.cgu.edu.tw.
authors: Ting-Wen
authors: TW
authors: Chen
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. csardas@gmail.com.
authors: Ruei-Chi
authors: RC
authors: Gan
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. ian.yfchang@gmail.com.|Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan. ian.yfchang@gmail.com.
authors: Yi-Feng
authors: YF
authors: Chang
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. pettliao@mail.cgu.edu.tw.
authors: Wei-Chao
authors: WC
authors: Liao
authors: Sequencing Technology Ltd, Taipei, Taiwan. g39328006@ym.edu.tw.
authors: Timothy H
authors: TH
authors: Wu
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. chichinglee@mail.cgu.edu.tw.
authors: Chi-Ching
authors: CC
authors: Lee
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. pjhuang@mail.cgu.edu.tw.
authors: Po-Jung
authors: PJ
authors: Huang
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. ejmiss@mail.cgu.edu.tw.
authors: Cheng-Yang
authors: CY
authors: Lee
authors: Department of Microbiology and Immunology, Chang Gung University, Taoyuan, Taiwan. mchen@mail.cgu.edu.tw.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan. mchen@mail.cgu.edu.tw.
authors: Yi-Ywan M
authors: YY
authors: Chen
authors: Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan. chchiu@adm.cgmh.org.tw.
authors: Cheng-Hsun
authors: CH
authors: Chiu
authors: Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan. petang@mail.cgu.edu.tw.|Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan. petang@mail.cgu.edu.tw.|Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan. petang@mail.cgu.edu.tw.
authors: Petrus
authors: P
authors: Tang
mesh_terms: D020137:Base Pair Mismatch / Q000235:genetics; D020029:Base Pairing / Q000235:genetics; D020451:Contig Mapping; D004926:Escherichia coli / Q000235:genetics*; D015723:Gene Library; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054643:INDEL Mutation / Q000235:genetics; D012015:Reference Standards; D013291:Streptococcus / Q000235:genetics*