title: GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.
abstract: Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements.
  
  
  
  Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa.
  
  
  
  GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.|Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.|Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
authors.forename: Lina
authors.initials: L
authors.lastname: Yuan
authors.affiliation: School of Life Sciences, Liaoning University, Shenyang, 110036, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yu
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Yanmin
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Beijing SpeedyCloud Technologies Co., Ltd., Beijing, 110036, China.
authors.forename: Yulai
authors.initials: Y
authors.lastname: Li
authors.affiliation: Department of Otolaryngology, Beijing Geriatric Hospital, Beijing, 100095, China.
authors.forename: Changqing
authors.initials: C
authors.lastname: Li
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Rujiao
authors.initials: R
authors.lastname: Li
authors.affiliation: Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.affiliation: Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China.
authors.forename: Gilman Kit-Hang
authors.initials: GK
authors.lastname: Siu
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.|Suzhou Institute of Systems Medicine, Suzhou, 215123, China.
authors.forename: Taijiao
authors.initials: T
authors.lastname: Jiang
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. xiaojf@big.ac.cn.
authors.forename: Jingfa
authors.initials: J
authors.lastname: Xiao
authors.affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. kangy@big.ac.cn.
authors.forename: Yu
authors.initials: Y
authors.lastname: Kang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods*; D011387:Prokaryotic Cells / Q000378:metabolism*; D015203:Reproducibility of Results
keywords: Core-gene-defined Genome Organizational Framework (cGOF); Prokaryotic genome; Rearrangement; Scaffolding