Please use this identifier to cite or link to this item:
http://hdl.handle.net/10397/66017
Title: | GAAP : Genome-organization-framework-assisted assembly pipeline for prokaryotic genomes | Authors: | Yuan, L Yu, Y Zhu, Y Li, Y Li, C Li, R Ma, Q Siu, GK Yu, J Jiang, T Xiao, J Kang, Y |
Issue Date: | 2017 | Source: | BMC genomics, 2017 , v. 18, suppl. 1, 952, p. 1-8 | Abstract: | Background: 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. Results: 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. Conclusions: 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. |
Keywords: | Core-gene-defined Genome Organizational Framework (cGOF) Prokaryotic genome Rearrangement Scaffolding |
Publisher: | BioMed Central | Journal: | BMC genomics | EISSN: | 1471-2164 | DOI: | 10.1186/s12864-016-3267-0 | Rights: | © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The following publication Yuan, L., Yu, Y., Zhu, Y., Li, Y., Li, C., Li, R., … Kang, Y. (2017). GAAP : Genome-organization-framework-assisted assembly pipeline for prokaryotic genomes. BMC Genomics, 18(Suppl. 1), 952, 1-8 is available at https://dx.doi.org/10.1186/s12864-016-3267-0 |
Appears in Collections: | Journal/Magazine Article |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
Yuan_Gaap_Genome_Organization.pdf | 671.09 kB | Adobe PDF | View/Open |
Page views
220
Last Week
5
5
Last month
Citations as of Sep 22, 2024
Downloads
103
Citations as of Sep 22, 2024
SCOPUSTM
Citations
7
Last Week
0
0
Last month
Citations as of Sep 26, 2024
WEB OF SCIENCETM
Citations
6
Last Week
0
0
Last month
Citations as of Jun 20, 2024
Google ScholarTM
Check
Altmetric
Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.